R/app_ui.R
In ShinyFabio/OliveHealthR2: A Shiny App for statistical and graphical analysis of data from the Olivehealth project
Defines functions
golem_add_external_resources
app_ui
#' The application User-Interface
#'
#' @param request Internal parameter for `{shiny}`.
#' DO NOT REMOVE.
#' @import shiny
#' @import shinydashboard
#' @import shinyWidgets
#' @importFrom plotly plotlyOutput
#' @import tmap
#' @import tmaptools
#' @import htmltools
#' @importFrom DT DTOutput
#' @importFrom shinycssloaders withSpinner
#' @importFrom shinyjs hidden
#' @importFrom InteractiveComplexHeatmap InteractiveComplexHeatmapOutput
#' @noRd
app_ui <- function(request) {
tagList(
tags$head(tags$style(type = 'text/css', ".navbar-default{display:none;}")), #rimuove la barra "Home | Codice"
# Leave this function for adding external resources
golem_add_external_resources(),
shinyjs::useShinyjs(),
# Your application UI logic
navbarPage(title = "OliveHealthR", theme = "www/spacelab.min.css",
id = "navb1",
#margin-right:auto; margin-left:auto;
tags$head(tags$style(type = "text/css", ".container-fluid{padding-left:0px; padding-right:0px ; }")),
tabPanel(title = "Welcome", value = "panel1",
tags$img(src = "www/Photo_2.jpg", width = "100%"),
h2(strong("Cos'è OliveHealthR?"), style = "text-align: center"),
br(), br(),
fluidRow(
column(1, offset=1,tags$img(src = "www/OliveHealthRfavicon.png", width = "173", height = "200")),
column(width = 6, offset = 1,
p(h4("OliveHealthR è un software che svolge analisi sui dati provenienti dal progetto OliveHealth. L'obiettivo principale del progetto è quello di identificare le
componenti salutistiche (es. polifenoli) in prodotti della filiera olivicola (quali foglie, drupe e
olio) correlandole alla geo-localizzazione di ciascun appezzamento. Sulla base di queste informazioni
verranno prodotti dataset delle variabili rappresentative delle principali caratteristiche fenotipiche,
biochimiche e genetiche associate all’ulivo dalle quali nascerà un database messo a disposizione ai
produttori olivicoli campani.", "Per maggiori informazioni sul progetto clicca",
strong(a(href = "https://olivehealth.it", "qui", .noWS = "after"), .noWS = "after"),
".", style = "font-family:'Quicksand', Sans-serif; font-weight: 400; line-height: 1.5; text-align: justify;"
)),
),
column(1, offset = 1, tags$img(src = "www/Olivehealt_Logo.png", width = "200", height = "200"))
),
fluidRow(column(1, offset = 5,
br(),
actionButton("jumpToP2", label = HTML(" VAI!"), icon("rocket"), class = "btn btn-primary btn-lg", width = "200px", style='padding:10px; font-size:200%; font-weight: bold;')
)
),
p(h4("Questo progetto è stato finanziato da:")),
fluidRow(
column(1, tags$img(src = "www/Logo_AprolCampania.jpg", width = "225", height = "150")),
column(2, offset = 4, tags$img(src = "www/CNR.png", width = "150", height = "155")),
column(3, offset = 2, tags$img(src = "www/stringa-2.png", width = "423", height = "110"))
)
),
##### Lista menuItem ####
tabPanel(title = "Codice", value = "panel2",
shinyBS::bsModal("keybutton_modal", "Inserisci codice", trigger = "keybutton", size = "small",
br(),textInput("ins_passw", label = "", placeholder = "Scrivi qui il codice.")),
dashboardPage(
dashboardHeader(title = "OliveHealthR",
tags$li(class = "dropdown",
actionBttn("keybutton", icon = icon("key"), style = "stretch", size = "lg" , color = "primary"),
actionBttn("jumptohome", icon = icon("home"), style = "stretch", size = "lg" , color = "primary")
)),
dashboardSidebar(
sidebarMenu(
menuItem("File", tabName = "filemenuitem", icon = icon("file-import")),
menuItem("Azienda", tabName = "azienda", icon = icon("id-card")),
menuItem("Campionamento azienda", tabName = "campazienda", icon = icon("file-alt"),
menuSubItem("Drupe e foglie", tabName = "drupleafsub"),
menuSubItem("Olio", tabName = "oliosub"),
menuSubItem("Calendario campionamenti", tabName = "calendar"),
shinyjs::hidden(menuSubItem("Analisi sensoriali", tabName = "assaggsub"))),
menuItem("Analisi laboratorio", tabName = "anlab", icon = icon("flask"),
menuSubItem("Polifenoli totali", tabName = "totpolsub"),
menuSubItem("Polifenoli individuali", tabName = "inpolsub"),
shinyjs::hidden(menuSubItem("Polifenoli LCxLC", tabName = "lcpolsub")),
menuSubItem("Analisi morfometrica", tabName = "anmorfosub")),
menuItem("Integrazione dati", tabName = "integrdati", icon = icon("vials"))
)
),
dashboardBody(
tabItems(
##### tabitem File ####
tabItem(tabName = "filemenuitem",
fluidRow(
#schede aziende
column(3,
box(width = NULL, status = "primary", title = h3(strong("Aziende"), style = "color: white; display:inline; margin-top: 0px;margin-bottom: 0px;"), solidHeader = T,
uiOutput("valbox_aziende")
)
),
#schede campionamento
column(3,
box(width = NULL, status = "primary", title = h3(strong("Schede campionamento"), style = "color: white; display:inline; margin-top: 0px;margin-bottom: 0px;"), solidHeader = T,
uiOutput("valbox_drupecamp"),
uiOutput("valbox_oliocamp"),
uiOutput("valbox_assaggi")
)
),
#polifenoli
column(3,
box(width = NULL, status = "primary", title = h3(strong("Polifenoli"), style = "color: white; display:inline; margin-top: 0px;margin-bottom: 0px;"), solidHeader = T,
uiOutput("valbox_poltot"),
uiOutput("valbox_polind")
)
),
#morfometria
column(3,
box(width = NULL, status = "primary", title = h3(strong("Morfometria"), style = "color: white; display:inline; margin-top: 0px;margin-bottom: 0px;"), solidHeader = T,
uiOutput("valbox_morfo"))
)
), #end of fluidrow
fluidRow(
column(4, offset = 4, style = "text-align:center;", br(), br(), br(), br(), br(),
actionButton("load_files", label = HTML(" Carica tutti dati!"), icon("file-upload"), class = "btn btn-primary btn-lg", width = "300px", style='padding:10px; font-size:200%; font-weight: bold;')
)
)
),
##### tabItem Azienda ####
tabItem(tabName = "azienda",
tabBox(width = 12,
tabPanel(tagList(shiny::icon("table"), HTML(" Tabella")),
box(width = NULL, status = "primary", style = "overflow-x: scroll;",
DT::DTOutput("content")
)
#mod_update_data_ui("updataaziende")
),
tabPanel(tagList(shiny::icon("chart-bar"), HTML(" Cultivar")),
box(width=NULL, status = "primary", h4(htmlOutput("numcult"))),
br(),
fluidRow(
column(2,
box(width = NULL, status = "primary",
radioButtons("selplotcult", label = h4("Tipo di grafico"), choices = list("Grafico a torta" = 1, "Grafico a barre" = 2), selected = 2))
),
column(width=10, box(width=NULL, status = "primary", shinycssloaders::withSpinner(image = "www/running_olive.gif", uiOutput("cultplot"))))
)
),
#### dati meteo
tabPanel(
tagList(shiny::icon("cloud-sun-rain"), HTML(" Dati meteo")),
sidebarLayout(
sidebarPanel(
width = 2,
selectInput("varmeteo",
label = tags$span("Variabile meteo", circleButton("hintmeteo", icon = icon("info"), status = "info", size = "xs")),
choices = c("Precipitazioni totali" = "tp",
"Volume d'acqua nel suolo (7-28cm)" = "swvl2",
"Volume d'acqua nel suolo (28-100cm)" = "swvl3")
),
shinyBS::bsPopover(
id = "hintmeteo",
title = "Variabili meteo",
content = paste0(
"Per ulteriori informazioni sulle misure di precipitazione clicca sul seguente link ",
a("copernicus.eu", href = "https://cds.climate.copernicus.eu/cdsapp#!/dataset/reanalysis-era5-land-monthly-means?tab=overview", target="_blank")
),
placement = "right",
trigger = c("hover","click"),
options = list(container = "body")
),
conditionalPanel(
condition = "input.tabsetmeteo == 'tabpanmeteomap'",
awesomeRadio("type_mapmeteo", "Tipo di mappa", choices = c("Statica","Animata")),
selectInput("selyearmeteo", "Seleziona anno", choices = "")
),
conditionalPanel(
condition = "input.tabsetmeteo == 'tabpanplotomap'",
awesomeRadio("meteoplot_tipoconf", "Tipo di confronto", choices = c("Tra anni", "Tra aziende"))
)
),
mainPanel(
width = 10,
tabsetPanel(id = "tabsetmeteo",
tabPanel("Mappa", value = "tabpanmeteomap",
conditionalPanel(condition = "input.type_mapmeteo == 'Animata'",
fluidPage(
shinycssloaders::withSpinner(imageOutput("mapmeteo"), image = "www/running_olive.gif"))
),
conditionalPanel(
condition = "input.type_mapmeteo == 'Statica'",
shinycssloaders::withSpinner(tmapOutput("mapmeteo2"))
)
),
tabPanel("Plot", value = "tabpanplotomap",
box(width=NULL, status = "primary",
fluidRow(
conditionalPanel(
condition = "input.meteoplot_tipoconf == 'Tra aziende'",
column(2, awesomeRadio("type_lineplot", "Tipo di grafico", choices = c("Statico","Animato"))),
column(3, selectInput("selyearplotmeteo", "Seleziona anno", choices = "Tutti")),
column(3, selectInput("selcod_plotmeteo", "Scegli una o più aziende", choices = "", multiple = TRUE))
),
conditionalPanel(
condition = "input.meteoplot_tipoconf == 'Tra anni'",
column(3, selectInput("selcod_plotmeteo2", "Scegli un'azienda", choices = ""))
)
)),
conditionalPanel(
condition = "input.type_lineplot == 'Statico'",
shinycssloaders::withSpinner(plotly::plotlyOutput("ggline_meteo"), image = "www/running_olive.gif")
),
conditionalPanel(
condition = "input.type_lineplot == 'Animato' && input.meteoplot_tipoconf == 'Tra aziende'",
shinycssloaders::withSpinner(imageOutput("plotline_animated"), image = "www/running_olive.gif")
)
)
)
)
)
), #end of tabbox dati meteo
# Mappa azienda
tabPanel(tagList(shiny::icon("map-marked-alt"), HTML(" Mappa")),
sidebarLayout(
sidebarPanel(width = 3,
div(actionButton("update", "Carica mappa", class = "btn-primary", style = 'padding:4px; font-size:160%'), align = "center"),
hr(),
selectInput("select3", "Seleziona la colonna da visualizzare", choices = "", multiple = FALSE),
selectInput("filt_cult_mapp", "Filtra per cultivar", choices = "", multiple = TRUE)
),
mainPanel(width = 9,
conditionalPanel(condition = "input.update != 0",
shinycssloaders::withSpinner(tmapOutput("map1",height = 650)),
)
)
)
)
) #end of tabset
),
##### TabItem Campionamento Azienda ####
##### campionamento foglie e drupe #########################################
tabItem(tabName = "drupleafsub",
tabBox(width = 12,
tabPanel(
tagList(shiny::icon("table"), HTML(" Tabella")),
#qui aggiungere la tabella drupe foglie
fluidPage(
box(width = NULL, status = "primary", style = "overflow-x: scroll;",
DT::DTOutput("tabledrupscheda")),
#mod_update_data_ui("updatadrupe")
)
),
tabPanel(tagList(shiny::icon("chart-bar"), HTML(" Grafici")),
#qui i grafici drupe foglie
sidebarLayout(
sidebarPanel(width = 2,
selectInput("selectx", "Seleziona la colonna X", choices = "", multiple = FALSE),
selectInput("selecty", "Seleziona la colonna Y", choices = "", multiple = FALSE)
),
mainPanel(width = 10,
tabsetPanel(
tabPanel("Scatter plot",
br(),
box(width=NULL, status = "primary",
fluidRow(
column(3, selectInput("selyearscatter", "Seleziona l'anno", choices = "", multiple = FALSE)),
column(3, selectInput("num2", "Scegli il numero di campionamento", choices = c("1" = "R1", "2" = "R2"), selected = "R1", multiple = FALSE)),
column(3, selectInput("selectfill", "Colonna da usare come riempimento", choices = "", multiple = FALSE))
)),
shinycssloaders::withSpinner(plotly::plotlyOutput("plotxy"), image = "www/running_olive.gif")
),
tabPanel("Barplot",
fluidRow(column(width = 2, br(),
box(width = NULL, status = "primary", checkboxGroupInput("checkcamp", "Seleziona campionamento", choices = ""))
),
column(width = 10, br(),
box(width=NULL, status = "primary",
shinycssloaders::withSpinner(plotly::plotlyOutput("barplot1"), image = "www/running_olive.gif"))
)
)
)#end of tabpanel
)#end of tabset
)#end of mainpanel
)#end of sidebarlayout
), #end of tabpanel grafici
tabPanel(tagList(shiny::icon("images"), HTML(" Galleria")),
#qui le foto drupe foglie
fluidPage(
fluidRow(
column(width=4,
fluidRow(
column(6,
box(width = NULL, status = "primary",
radioGroupButtons(inputId = "campfoto", label = "Numero campionamento", choices = c("1" = "1_campionamento", "2" = "2_campionamento"),
individual = TRUE, checkIcon = list(yes = tags$i(class = "fa fa-circle", style = "color: steelblue"), no = tags$i(class = "fa fa-circle-o", style = "color: steelblue")))
)
),
column(6, box(width=NULL, status = "primary",
selectInput("selyearfoto", "Seleziona l'anno", choices = "", multiple = FALSE)
))
),
fluidRow(column(12, box(width=NULL, status = "primary", style = "overflow-x: scroll;", DT::DTOutput("prov2"))))
),
conditionalPanel(condition = "input.prov2_rows_selected == 0",
p(strong(h4("Per favore seleziona un'azienda dalla tabella", align = "center")))
),
conditionalPanel(condition = "input.prov2_rows_selected != 0",
column(width = 4, box(width=NULL, status = "primary", title = "Foglie", align= "center", uiOutput("phfoglia"))),
column(width = 4, box(width=NULL, status = "primary", title = "Drupe",align = "center", uiOutput("phdrupa")))
)
) #end of fluidRow
)
), #end of tabpanel foto
tabPanel(tagList(shiny::icon("map-marked-alt"), HTML(" Mappa")),
mod_render_map_ui("modulo_mappa_datadrupe")
) #end of tabpanel mappa drupe foglie
) #end of tabBox
), #end of tabitem drupe foglie
##### campionamento olio #########################################
tabItem(tabName = "oliosub",
tabBox(width = 12,
tabPanel(tagList(shiny::icon("table"), HTML(" Tabella")),
#qui aggiungere la tabella drupe foglie
fluidPage(
box(width = NULL, status = "primary", style = "overflow-x: scroll;",
DT::DTOutput("tableolioscheda")),
)
),
tabPanel(tagList(shiny::icon("map-marked-alt"), HTML(" Mappa")),
sidebarLayout(
sidebarPanel(
width = 3,
div(actionButton("updateoilmap", "Carica mappa", class = "btn-primary", style = 'padding:4px; font-size:160%'), align = "center"),
conditionalPanel(condition = "input.updateoilmap != 0",
hr(),
selectInput("selcoloilmap", "Seleziona la colonna da visualizzare", choices = "", multiple = FALSE),
selectInput("selyearoilmap", "Seleziona l'anno", choices = "", multiple = FALSE)
)
),
mainPanel(width = 9,
conditionalPanel(condition = "input.updateoilmap != 0",
shinycssloaders::withSpinner(tmapOutput("mapolio"))),
)
)
)
)
),
##### Calendario #########
tabItem(tabName = "calendar",
sidebarLayout(
sidebarPanel(width = 2,
awesomeRadio("selfilecalend", "Seleziona il tipo di campionamento", choices = ""),
conditionalPanel(condition = "input.selfilecalend == 'Drupe e foglie'",
awesomeRadio("selcampcalend", "Seleziona il numero di campionamento", choices = c("Entrambi", "R1", "R2")),
),
selectInput("selyearcalend", "Seleziona l'anno", choices = "", multiple = FALSE),
selectInput("selaziendacalend", "Scegli l'azienda", choices = "", multiple = FALSE),
),
mainPanel(width = 10,
shinycssloaders::withSpinner(image = "www/running_olive.gif",plotOutput("yearcalendar", height = "700px"))
)
)
),
###### Assaggi sensoriali ########
tabItem(tabName = "assaggsub",
tabBox(width = 12,
#tabella
tabPanel(tagList(shiny::icon("table"), HTML(" Tabella")),
box(width = NULL, status = "primary", style = "overflow-x: scroll;",
DT::DTOutput("tableassaggischeda")),
),
#grafici
tabPanel(
tagList(shiny::icon("chart-bar"), HTML(" Grafici")),
tabsetPanel(
tabPanel("Scatter plot",
sidebarLayout(
sidebarPanel(width = 2,
selectInput("selectxassaggiscatt", "Seleziona la colonna X", choices = "", multiple = FALSE),
selectInput("selectyassaggiscatt", "Seleziona la colonna Y", choices = "", multiple = FALSE),
),
mainPanel(width = 10,
br(),
box(width=NULL, status = "primary",
fluidPage(
fluidRow(
column(3, selectInput("selyearscatterassagg", "Seleziona l'anno", choices = "", multiple = FALSE)),
column(3, selectInput("selectfillassaggi", "Colonna da usare come riempimento", choices = "", multiple = FALSE))
))),
shinycssloaders::withSpinner(image = "www/running_olive.gif", plotly::plotlyOutput("scattplotassagg"))
)
)
), #end of tabpanel scatter plot
tabPanel("Barplot",
sidebarLayout(
sidebarPanel(width = 2,
awesomeRadio("barplotassaggi", "Tipo di barplot", choices = c("Affiancato" = "dodge", "Impilato" = "stack")),
selectInput("selyearbarassagg", "Seleziona l'anno", choices = "", multiple = FALSE),
),
mainPanel(width = 10,
br(),
shinycssloaders::withSpinner(image = "www/running_olive.gif", plotly::plotlyOutput("barplotassagg"))
)
)
), #end of tabpanel barplot
tabPanel("Spiderplot",
sidebarLayout(
sidebarPanel(width = 2,
selectInput("selyearspiderassaggi", "Seleziona l'anno", choices = "", multiple = FALSE),
selectInput("selcodspiderassaggi1", "Seleziona un'azienda", choices = "", multiple = FALSE),
awesomeCheckbox("addcodspiderassaggi", "Aggiungi seconda azienda", value = FALSE),
conditionalPanel(condition = "input.addcodspiderassaggi == true",
selectInput("selcodspiderassaggi2", "Seleziona un'azienda", choices = "", multiple = FALSE)
)
),
mainPanel(width = 10,
div(shinycssloaders::withSpinner(image = "www/running_olive.gif", plotOutput("assaggispider", width = "100%",height = "600px")), align = "center"),
)
)
) #end of tabpanel spiderplot
) #end of tabsetpanel
), #end of tabpanel grafici
#galleria
tabPanel(tagList(shiny::icon("images"), HTML(" Galleria")),
fluidPage(
fluidRow(
column(width=4,
fluidRow(
column(6, box(width=NULL, status = "primary",
selectInput("selyearallegatph", "Seleziona l'anno", choices = "", multiple = FALSE))
)
),
fluidRow(column(12, box(width=NULL, status = "primary", DT::DTOutput("dtallegato"))))
),
column(width = 8,
column(width = 6, offset = 3,
conditionalPanel(condition = "input.dtallegato_rows_selected == 0",
box(width = NULL, background = "yellow", tags$i(class = "fas fa-exclamation-triangle", style="font-size: 27px"), h4(strong("Seleziona un'azienda dalla tabella"), style = "color: white"), style = "text-align: justify; text-align: center;"),
)
),
conditionalPanel(condition = "input.dtallegato_rows_selected != 0",
uiOutput("phallegati")
)
)
) #end of fluidRow
)
),
#mappa
tabPanel(tagList(shiny::icon("map-marked-alt"), HTML(" Mappa")),
mod_render_map_ui("modulo_mappa_assaggi")
) #end of tabpanel mappa assaggi
) #end of tabBox
), #end of tabItem
##### TabItem Analisi Laboratorio #####
# Tab polifenoli totali ----------------------------------------------------------------
tabItem(tabName = "totpolsub",
sidebarLayout(
sidebarPanel(width = 2,
radioGroupButtons("selfilepoltot", "Seleziona i polifenoli da analizzare",
choiceValues = list("foglie", "drupe", "olio", "posa", "sansa"),
choiceNames = list(
paste(shiny::icon("leaf", style='font-size:16px;'), HTML("<b style=font-size:16px> Foglie</b>")),
paste(tags$img(src = "www/olive_icon2.png", height = "22px", width = "22px"), HTML("<b style=font-size:16px> Drupe</b>")),
paste(tags$img(src = "www/olive_oil.png", height = "22px", width = "22px"), HTML("<b style=font-size:16px> Olio</b>")),
paste(tags$img(src = "www/posa.png", height = "22px", width = "22px"), HTML("<b style=font-size:16px> Posa</b>")),
paste(tags$img(src = "www/sansa3.png", height = "23px", width = "23px"), HTML("<b style=font-size:16px> Sansa</b>"))),
direction = "vertical", justified = TRUE, status = "primary"
),
hr(),
conditionalPanel(condition = "input.tabboxpoltot == 'tabdtpoltot' || (input.tabboxpoltot == 'tabpoltotgraph' && input.boxpoltotgraph == 'boxscattpoltot')",
materialSwitch(inputId = "summpoltot", label = "Sintetizza i dati", value = TRUE, status = "primary")
),
conditionalPanel(
condition = "input.tabboxpoltot == 'tabpoltotgraph'",
h4(strong("Impostazioni grafici")),
#scatterplot
conditionalPanel(condition = "input.boxpoltotgraph == 'boxscattpoltot'",
selectInput("selectxtot", "Seleziona la colonna X", choices = "", multiple = FALSE),
selectInput("selectytot", "Seleziona la colonna Y", choices = "", multiple = FALSE)
),
#barplot
conditionalPanel(condition = "input.boxpoltotgraph == 'boxbarpoltot'",
selectInput("selectytotbar", "Seleziona la colonna Y", choices = "", multiple = FALSE),
selectInput("selectfilltotbar", "Colonna da usare come riempimento", choices = c("N_campionamento", "Cultivar_principale"), selected = "N_campionamento"),
hr(),
checkboxGroupInput("checkcamptot", "Seleziona campionamento", choices = "")
)
),
# MAPPA __________________________________________________________
conditionalPanel(condition = "input.tabboxpoltot == 'tabpoltotmap'",
div(actionButton("updatepoltotmap", "Carica mappa", class = "btn-primary", style = 'padding:4px; font-size:160%'), align = "center"),
conditionalPanel(condition = "input.updatepoltotmap != 0",
hr(),
selectInput("colpoltotmap1", "Seleziona la colonna da visualizzare", choices = "", multiple = FALSE),
selectInput("yearpoltotmap1", "Seleziona l'anno", choices = "", multiple = FALSE),
selectInput("numpoltotmap1", "Scegli il numero di campionamento", choices = "", multiple = FALSE),
hr(),
div(actionButton("addmappoltot2", label = "Aggiungi seconda mappa"), align = "center"),
),
conditionalPanel(condition = "input.addmappoltot2 != 0",
br(),
selectInput("colpoltotmap2", "Seleziona la colonna da visualizzare", choices = "", multiple = FALSE),
selectInput("yearpoltotmap2", "Seleziona l'anno", choices = "", multiple = FALSE),
selectInput("numpoltotmap2", "Scegli il numero di campionamento", choices = "", multiple = FALSE),
)
)
),
mainPanel(width = 10,
tabBox(id = "tabboxpoltot", width = NULL,
tabPanel(tagList(shiny::icon("table"), HTML(" Tabella")), value = "tabdtpoltot",
fluidPage(
box(width = NULL, status = "primary", style = "overflow-x: scroll;",
DT::DTOutput("tablepoltot")),
#mod_update_data_ui("updatapol"),
br(),
mod_render_NAbox_ui("naboxpoltot")
)
), #end of tabpanel tabella
tabPanel(tagList(shiny::icon("chart-bar"), HTML(" Grafici")), value = "tabpoltotgraph",
tabsetPanel(id = "boxpoltotgraph",
tabPanel("Scatter plot", value = "boxscattpoltot",
box(width=NULL, status = "primary",
fluidRow(
column(3, selectInput("selyearscattertot", "Seleziona l'anno", choices = "", multiple = FALSE)),
column(3, selectInput("numtot", "Scegli il numero di campionamento", choices = "", multiple = FALSE)),
column(3, selectInput("selectfilltot", "Colonna da usare come riempimento", choices = "", multiple = FALSE))
)),
shinycssloaders::withSpinner(image = "www/running_olive.gif", plotly::plotlyOutput("totscatplot"))
), #end of tabpanel scatter plot
tabPanel("Barplot", value = "boxbarpoltot",
shinycssloaders::withSpinner(image = "www/running_olive.gif", plotly::plotlyOutput("barplottot"))
) #end of tabpanel barplot
) #end of tabsetpanel grafici
), #end of tabpanel grafici
#tabpanel mappa
tabPanel(tagList(shiny::icon("map-marked-alt"), HTML(" Mappa")), value = "tabpoltotmap",
conditionalPanel(condition = "input.updatepoltotmap != 0",
shinycssloaders::withSpinner(tmapOutput("poltotmap1"))),
conditionalPanel(condition = "input.addmappoltot2 != 0",
hr(),
shinycssloaders::withSpinner(tmapOutput("poltotmap2")))
)
) #end of tabbox poltot
) #end of mainpanel
)#end of sidebarlayout
), #end of tabitem "totpolsub"
# Tab polifenoli individuali ----------------------------------------------------------------------------
tabItem(tabName = "inpolsub",
sidebarLayout(
sidebarPanel(width = 2,
radioGroupButtons("selfilepolind", "Seleziona i polifenoli da analizzare",
choiceValues = list("foglie", "drupe", "olio", "posa"),
choiceNames = list(
paste(icon("leaf", style='font-size:16px;'), HTML("<b style=font-size:16px> Foglie</b>")),
paste(tags$img(src = "www/olive_icon2.png", height = "22px", width = "22px"), HTML("<b style=font-size:16px> Drupe</b>")),
paste(tags$img(src = "www/olive_oil.png", height = "22px", width = "22px"), HTML("<b style=font-size:16px> Olio</b>")),
paste(tags$img(src = "www/posa.png", height = "22px", width = "22px"), HTML("<b style=font-size:16px> Posa</b>"))
),
direction = "vertical", justified = TRUE, status = "primary"
),
hr(),
conditionalPanel(
condition = "input.tabboxpolind == 'tabdtpolind' || input.tabboxpolind == 'tabpolindpca' ||
(input.tabboxpolind == 'tabpolindgraph' && input.boxpolindgraph == 'boxscattpolind' )",
materialSwitch(inputId = "summpolind", label = "Sintetizza i dati", value = TRUE, status = "primary")
),
conditionalPanel(
condition = "input.tabboxpolind == 'tabpolindgraph'",
h4(strong("Impostazioni grafici")),
# Scatterplot ______________________________________________________
conditionalPanel(condition = "input.boxpolindgraph == 'boxscattpolind'",
selectInput("selectxind", "Seleziona la colonna X", choices = "", multiple = FALSE),
selectInput("selectyind", "Seleziona la colonna Y", choices = "", multiple = FALSE)
),
# Boxplot ______________________________________________________
conditionalPanel(condition = "input.boxpolindgraph == 'boxboxplotpolind'",
selectInput("selectyboxind", "Seleziona un polifenolo", choices = "", multiple = FALSE)
),
# Barplot ____________________________________________________________
conditionalPanel(condition = "input.boxpolindgraph == 'boxbarpolind'",
selectInput("selectyindbar", "Seleziona un polifenolo", choices = "", multiple = FALSE),
selectInput("selectfillindbar", "Colonna da usare come riempimento", choices = c("N_campionamento", "Cultivar_principale"), selected = "N_campionamento"),
hr(),
checkboxGroupInput("checkcampind", "Seleziona campionamento", choices = "")
),
# Heatmap _______________________________________________________
conditionalPanel(condition = "input.boxpolindgraph == 'boxheatpolind'",
div(actionButton("updateheat", label = "Carica!", class = "btn btn-primary btn-lg", width = "140px", style='padding:5px; font-size:150%; font-weight: bold;'), align= "center"),
br(),
h4(strong("Dati")),
selectInput("numheat", "Scegli il numero di campionamento", choices = "", multiple = FALSE),
selectInput("selyearheatind", "Seleziona l'anno", choices = "", multiple = FALSE),
hr(),
h4(strong("Preprocessing")),
selectInput("selscaleheat", "Scala i dati:", choices = c("No" = "none", "Per riga" = "row", "Per colonna" = "column"), selected = "none"),
hr(),
h4(strong("Opzioni dendrogramma")),
###voglio il dendrograma su riga o colonna o entrambi?
h5(strong("Scegli dove mostrare il dendrogramma")),
fluidRow(
column(6, materialSwitch(inputId = "rowdend", label = "Riga", value = TRUE, status = "primary", width = "90%")),
column(6, materialSwitch(inputId = "columndend", label = "Colonna", value = TRUE, status = "primary", width = "90%"))
),
selectInput("selectannot", "Colonna annotazione:", choices = c("Provincia", "Cultivar_principale", "Areale")),
conditionalPanel(condition = "input.rowdend == 1 || input.columndend == 1",
selectInput("seldistheatpol", "Funzione di distanza:", choices = c("euclidean", "maximum", "manhattan", "canberra", "minkowski"), selected = "euclidean"),
selectInput("selhclustheatpol", "Metodo clustering:", choices = c("ward.D", "ward.D2", "single", "complete", "average" , "mcquitty", "median", "centroid"), selected = "complete"),
),
conditionalPanel(condition = "input.rowdend == 0",
h5(strong("Ordinare i dati per annotazione?")),
awesomeCheckbox("heatsort", label = "Ordina", value = TRUE)
),
conditionalPanel(condition = "input.rowdend == 1",
hr(),
h4(strong("Dendrogramma su riga")),
sliderInput("sliderrowheat", "Numero cluster:", min = 2, max = 10, value = 2),
),
conditionalPanel(condition = "input.columndend == 1",
hr(),
h4(strong("Dendrogramma su colonna")),
uiOutput("sliderheatcol"),
)
), #end of conditional heatmap
# Spiderplot __________________________________________
conditionalPanel(condition = "input.boxpolindgraph == 'boxspiderpolind'",
awesomeRadio("type_spidind", "Tipo di confronto", choices = c("Tra aziende","Tra anni")),
#confronto tra aziende
conditionalPanel(condition = "input.type_spidind == 'Tra aziende'",
selectInput("selyearspiderpolind", "Seleziona l'anno", choices = "", multiple = FALSE),
selectInput("selcampspiderpolind", "Seleziona il numero di campionamento", choices = "", multiple = FALSE),
selectInput("selcodspiderpolind", "Seleziona un'azienda", choices = "", multiple = FALSE),
awesomeCheckbox("addcodspiderpolind", "Aggiungi seconda azienda", value = FALSE),
conditionalPanel(condition = "input.addcodspiderpolind == true",
selectInput("selcodspiderpolind2", "Seleziona un'azienda", choices = "", multiple = FALSE)
)
),
#confronto tra anni
conditionalPanel(
condition = "input.type_spidind == 'Tra anni'",
selectInput("selcodspidind", "Seleziona un'azienda", choices = "", multiple = FALSE),
selectInput("selcampspidind", "Seleziona il numero di campionamento", choices = "", multiple = FALSE)
)
),
# Correlation _________________________________________________________________
conditionalPanel(
condition = "input.boxpolindgraph == 'boxcorrpolind'",
selectInput("selyearcorrind", "Seleziona l'anno", choices = "", multiple = FALSE),
selectInput("numcorr", "Scegli il numero di campionamento", choices = "", multiple = FALSE)
),
), #end of conditional panel dei grafici
# PCA ____________________________________________________________________
conditionalPanel(
condition = "input.tabboxpolind == 'tabpolindpca'",
selectInput("selyearpca", "Seleziona l'anno", choices = "", multiple = FALSE),
selectInput("numpca", "Scegli il numero di campionamento", choices = "", multiple = FALSE),
radioGroupButtons(inputId = "selcorpca", label = "Matrice:", choices = c("Correlazione" = TRUE, "Covarianza" = FALSE),
individual = TRUE, checkIcon = list(yes = tags$i(class = "fa fa-circle", style = "color: steelblue"),no = tags$i(class = "fa fa-circle-o", style = "color: steelblue")))
),
# CLUSTERING _____________
conditionalPanel(
condition = "input.tabboxpolind == 'tabclustpolind'",
selectInput("selcolclustpolind", "Seleziona variabile", choices = c("Codice_azienda", "Cultivar_principale")),
selectInput("selyearclustpolind", "Seleziona l'anno", choices = "", multiple = TRUE),
selectInput("numclustpolind", "Scegli il numero di campionamento", choices = "", multiple = FALSE),
#materialSwitch(inputId = "summarizeclustmorfo", label = "Sintetizza i dati", status = "primary", value = TRUE),
radioGroupButtons("selclustmethodpolind", "Tipo di clustering", choices = c("Gerarchico", "Partizionale"), justified = TRUE, status = "primary"),
conditionalPanel(
condition = "input.selclustmethodpolind == 'Partizionale'",
selectInput("selclusthpolind", "Seleziona l'algoritmo di clustering", choices = c("K-means", "PAM", "Clara"), selected = "K-means", multiple = FALSE),
)
),
# MAPPA __________________________________________________________
conditionalPanel(condition = "input.tabboxpolind == 'tabpolindmap'",
div(actionButton("updatepolindmap", "Carica mappa", class = "btn-primary", style = 'padding:4px; font-size:160%'), align = "center"),
conditionalPanel(condition = "input.updatepolindmap != 0",
hr(),
selectInput("colpolindmap1", "Seleziona la colonna da visualizzare", choices = "", multiple = FALSE),
selectInput("yearpolindmap1", "Seleziona l'anno", choices = "", multiple = FALSE),
selectInput("numpolindmap1", "Scegli il numero di campionamento", choices = "", multiple = FALSE),
hr(),
div(actionButton("addmappolind2", label = "Aggiungi seconda mappa"), align = "center"),
),
conditionalPanel(condition = "input.addmappolind2 != 0",
br(),
selectInput("colpolindmap2", "Seleziona la colonna da visualizzare", choices = "", multiple = FALSE),
selectInput("yearpolindmap2", "Seleziona l'anno", choices = "", multiple = FALSE),
selectInput("numpolindmap2", "Scegli il numero di campionamento", choices = "", multiple = FALSE),
)
)
), #end of sidebarpanel
mainPanel(width = 10,
tabBox(id = "tabboxpolind", width = NULL,
tabPanel(tagList(shiny::icon("table"), HTML(" Tabella")), value = "tabdtpolind",
fluidPage(
box(width = NULL, status = "primary", style = "overflow-x: scroll;",
DT::DTOutput("tablepolind")),
mod_render_NAbox_ui("naboxpolind")
)
), #end of tabpanel tabella
tabPanel(tagList(shiny::icon("chart-bar"), HTML(" Grafici")), value = "tabpolindgraph",
tabsetPanel(id = "boxpolindgraph",
tabPanel("Scatter plot", value = "boxscattpolind",
box(width=NULL, status = "primary",
fluidRow(
column(3, selectInput("selyearscatterind", "Seleziona l'anno", choices = "", multiple = FALSE)),
column(3, selectInput("numind", "Scegli il numero di campionamento", choices = "", multiple = FALSE)),
column(3, selectInput("selectfillind", "Colonna da usare come riempimento", choices = "", multiple = FALSE))
)),
shinycssloaders::withSpinner(image = "www/running_olive.gif", plotly::plotlyOutput("scatterindpol"))
), #end of tabpanel scatterplot
tabPanel("Boxplot", value = "boxboxplotpolind",
box(width=NULL, status = "primary",
fluidRow(
column(3, selectInput("selyearboxind", "Seleziona l'anno", choices = "", multiple = FALSE)),
column(3, selectInput("numboxind", "Scegli il numero di campionamento", choices = "", multiple = FALSE)),
column(3, selectInput("selectfillboxind", "Colonna da usare come riempimento", choices = "", multiple = FALSE))
)),
shinycssloaders::withSpinner(image = "www/running_olive.gif", plotly::plotlyOutput("boxplotindpol"))
),
tabPanel("Barplot", value = "boxbarpolind",
shinycssloaders::withSpinner(image = "www/running_olive.gif", plotly::plotlyOutput("barplotind"))
), #end of tabpanel barplot
tabPanel("Heatmap", value = "boxheatpolind",
InteractiveComplexHeatmap::InteractiveComplexHeatmapOutput("heatmap_polind_output", layout = "1|(2-3)", width1 = 850, height1 = 550)
),
tabPanel("Correlation Plot", value = "boxcorrpolind",
shinycssloaders::withSpinner(image = "www/running_olive.gif", plotly::plotlyOutput("corrplotind"))
), #end of tabpanel correlation
tabPanel(
"Spiderplot",
value = "boxspiderpolind",
div(shinycssloaders::withSpinner(image = "www/running_olive.gif", plotOutput("spider_polind", width = "100%",height = "600px")), align = "center"),
)
) #end of tabsetpanel
), #end of tabPanel Grafici
tabPanel(tagList(shiny::icon("chart-line"), HTML(" PCA")), value = "tabpolindpca",
tabsetPanel(
tabPanel("Plot",
br(),
fluidPage(
fluidRow(
column(3, box(width = NULL, status = "primary",
awesomeRadio("selbiplotpolind", "Seleziona tipo di grafico", choices = c("Biplot", "Plot")))),
column(4, box(width = NULL, status = "primary",
selectInput("colbiplot", "Seleziona colonna riempimento", choices = c("Codice_azienda", "Cultivar_principale", "Azienda", "Provincia", "Areale")))),
column(4, box(width = NULL, status = "primary",
awesomeCheckboxGroup("shpbiplot", "Aggiungi geometria", choices = "Provincia", inline = TRUE)
))),
shinycssloaders::withSpinner(image = "www/running_olive.gif", plotly::plotlyOutput("biplot", height = "500px")))
),
tabPanel("Screeplot",
br(),
shinycssloaders::withSpinner(image = "www/running_olive.gif", plotly::plotlyOutput("screeplot", width = "75%"))
),
tabPanel("Loadings",
fluidPage(
br(),
fluidRow(column(4, box(width = NULL, status = "primary", uiOutput("sliderpc")))),
shinycssloaders::withSpinner(image = "www/running_olive.gif", plotly::plotlyOutput("loadings"))
)
),
tabPanel("Plot 3D",
fluidPage(
br(),
fluidRow(
column(4, box(width = NULL, status = "primary",
selectInput("col3dind", "Seleziona colonna riempimento", choices = c("Codice_azienda", "Provincia", "Cultivar_principale", "Areale"))))
),
shinycssloaders::withSpinner(image = "www/running_olive.gif", plotly::plotlyOutput("pca3dpolind", height = "500px"))
)
)
) #end of tabsetpanel
), #end of tabpanel PCA
# Clustering
tabPanel(
tagList(tags$img(src = "www/clustering_icon.png", height = "16px", width = "16px"), HTML(" Clustering")), value = "tabclustpolind",
tabsetPanel(
tabPanel("Cluster plot",
br(),
fluidPage(
fluidRow(
column(
4,
box(width = NULL, status = "primary",
sliderInput("selnumclustpolind", "Numero cluster:", min = 1, max = 10, value = 2))),
column(
4,
conditionalPanel(
condition = "input.selclustmethodpolind == 'Gerarchico'",
box(width=NULL, status = "primary",
selectInput("selhclustmethpolind", "Seleziona metodo agglomerazione", choices = c("single", "complete", "ward.D", "ward.D2"), selected = "ward.D2"))
)
)
),
shinycssloaders::withSpinner(image = "www/running_olive.gif", plotOutput("plotclusterpolind", height = "600px"))
)
),
tabPanel("Numero cluster",
br(),
shinycssloaders::withSpinner(image = "www/running_olive.gif", plotOutput("numclustergraphpolind", height = "800px"))
)
)
), #end of tabpanel clustering
#tab galleria (ovvero i cromatogrammi)
tabPanel(tagList(shiny::icon("images"), HTML(" Galleria")), value = "tabpolindcroma",
fluidPage(
fluidRow(
column(4,
fluidRow(
column(6,
box(width = NULL, status = "primary",
radioGroupButtons(inputId = "campcromatph", label = "Numero campionamento", choices = c("1" = "1_campionamento", "2" = "2_campionamento"),
individual = TRUE, checkIcon = list(yes = tags$i(class = "fa fa-circle", style = "color: steelblue"), no = tags$i(class = "fa fa-circle-o", style = "color: steelblue")))
)
),
column(6, box(width=NULL, status = "primary",
selectInput("selyearcromatph", "Seleziona l'anno", choices = "", multiple = FALSE))
)
),
fluidRow(column(12, box(width=NULL, status = "primary", DT::DTOutput("prov3"))))
),
column(8,
column(6, offset = 3,
conditionalPanel(condition = "input.prov3_rows_selected == 0",
box(width = NULL, background = "yellow", tags$i(class = "fas fa-exclamation-triangle", style="font-size: 27px"), h4(strong("Seleziona un'azienda dalla tabella"), style = "color: white"), style = "text-align: justify; text-align: center;")
),
#R1 e olio/posa
conditionalPanel(condition = "input.prov3_rows_selected != 0 && output.check_crompolind == 'no'",
box(width = NULL, background = "yellow", tags$i(class = "fas fa-exclamation-triangle", style="font-size: 27px"), h4(strong("I dati sull'olio e sulla posa riguardano solamente il secondo campionamento."), style = "color: white"), style = "text-align: justify; text-align: center;")
)
),
#non R1 e olio/posa
conditionalPanel(condition = "input.prov3_rows_selected != 0 && output.check_crompolind == 'yes'",
fluidRow(box(width=NULL, status = "primary", title = "Cromatogramma", align= "center", uiOutput("phcromat"))),
fluidRow(
box(width=NULL, status = "primary", title = "Polifenoli",align = "center", style = "overflow-x: scroll;",
DTOutput("tabcromatpolind")
)
)
) #end of conditional panel !=0
) #end of column 8
) #end of fluidRow
)
),
tabPanel(tagList(shiny::icon("map-marked-alt"), HTML(" Mappa")), value = "tabpolindmap",
conditionalPanel(condition = "input.updatepolindmap != 0",
shinycssloaders::withSpinner(tmapOutput("polindmap1"))),
conditionalPanel(condition = "input.addmappolind2 != 0",
hr(),
shinycssloaders::withSpinner(tmapOutput("polindmap2")))
)
)
)
)
), #end of tabitem "inpolsub"
# ####### Tab polifenoli LCxLC ##########
tabItem(tabName = "lcpolsub",
sidebarLayout(
sidebarPanel(width = 2,
radioGroupButtons("selfilepollc", "Seleziona i polifenoli da analizzare",
choiceValues = list("foglie", "drupe", "olio", "posa", "sansa"),
choiceNames = list(
paste(shiny::icon("leaf", style='font-size:16px;'), HTML("<b style=font-size:16px> Foglie</b>")),
paste(tags$img(src = "www/olive_icon2.png", height = "22px", width = "22px"), HTML("<b style=font-size:16px> Drupe</b>")),
paste(tags$img(src = "www/olive_oil.png", height = "22px", width = "22px"), HTML("<b style=font-size:16px> Olio</b>")),
paste(tags$img(src = "www/posa.png", height = "22px", width = "22px"), HTML("<b style=font-size:16px> Posa</b>")),
paste(tags$img(src = "www/sansa3.png", height = "23px", width = "23px"), HTML("<b style=font-size:16px> Sansa</b>"))),
direction = "vertical", justified = TRUE, status = "primary"
),
hr(),
# Tabella
conditionalPanel(condition = "input.tabboxlcxlc == 'tabdtlc'",
awesomeRadio("dttypelc", "Tipo di visualizzazione", choices = c("Wide", "Long"))
),
#Grafici
conditionalPanel(condition = "input.tabboxlcxlc == 'tabgraphlc'",
h4(strong("Impostazioni grafici")),
#scatterplot e barplot
conditionalPanel(condition = "input.boxlcgraph == 'tabpanscattlc' || input.boxlcgraph == 'tabpanbarlc'",
awesomeRadio("lcdatatypescatt", "Filtra i dati per:", choices = c("Azienda", "Polifenolo", "Cultivar principale")),
conditionalPanel(
condition = "input.lcdatatypescatt == 'Azienda'",
selectInput("lcselaziendascatt", "Scegli l'azienda", choices = "")
),
conditionalPanel(
condition = "input.lcdatatypescatt == 'Azienda' || input.lcdatatypescatt == 'Cultivar principale'",
awesomeCheckbox("logscattlc", "Scala logaritmica", value = TRUE)
),
conditionalPanel(
condition = "input.lcdatatypescatt == 'Polifenolo'",
selectInput("lcselpolifscatt", "Scegli il polifenolo", choices = "")
),
conditionalPanel(condition = "input.lcdatatypescatt == 'Cultivar principale'",
selectInput("lcselcultscatt", "Scegli la cultivar principale", choices = ""),
awesomeCheckbox("sintscattlc", "Sintetizza i dati", value = TRUE)
),
selectInput("numscattlc", "Scegli il numero di campionamento", choices = ""),
selectInput("fillscattlc", "Scegli colonna riempimento", choices = "")
),
conditionalPanel(condition = "input.boxlcgraph == 'tabpanbarlc' && input.lcdatatypescatt == 'Cultivar principale'",
awesomeRadio("bartypelc", "Tipo di barplot", choices = c("Affiancato" = "dodge", "Impilato" = "stack")),
selectInput("lcselpolbar", "Polifenoli da mostrare", choices = "")
),
# HEATMAP
conditionalPanel(condition = "input.boxlcgraph == 'tabpanheatlc'",
div(actionButton("updateheatlc", label = "Carica!", class = "btn btn-primary btn-lg", width = "140px", style='padding:5px; font-size:150%; font-weight: bold;'), align= "center"),
br(),
h4(strong("Dati")),
selectInput("numheatlc", "Scegli il numero di campionamento", choices = "", multiple = FALSE),
selectInput("cultheatlc", "Filtra per cultivar", choices = "", multiple = FALSE),
#selectInput("selyearheatmorfo", "Seleziona l'anno", choices = "", multiple = FALSE),
h4(strong("Preprocessing")),
selectInput("selscaleheatlc", "Scala i dati:", choices = c("No" = "none", "Per riga" = "row", "Per colonna" = "column"), selected = "none"),
hr(),
h4(strong("Opzioni dendrogramma")),
###voglio il dendrograma su riga o colonna o entrambi?
h5(strong("Scegli dove mostrare il dendrogramma")),
fluidRow(
column(6, materialSwitch(inputId = "rowdendlc", label = "Riga", value = TRUE, status = "primary", width = "90%")),
column(6, materialSwitch(inputId = "columndendlc", label = "Colonna", value = TRUE, status = "primary", width = "90%"))
),
selectInput("selectannotlc", "Colonna annotazione:", choices = c("Provincia", "Cultivar_principale")),
conditionalPanel(condition = "input.rowdendlc == 1 || input.columndendmorfo == 1",
selectInput("seldistheatlc", "Funzione di distanza:", choices = c("euclidean", "maximum", "manhattan", "canberra", "minkowski"), selected = "euclidean"),
selectInput("selhclustheatlc", "Metodo clustering:", choices = c("ward.D", "ward.D2", "single", "complete", "average" , "mcquitty", "median", "centroid"), selected = "complete"),
),
conditionalPanel(condition = "input.rowdendlc == 0",
h5(strong("Ordinare i dati per annotazione?")),
awesomeCheckbox("heatsortlc", label = "Ordina", value = TRUE)
),
conditionalPanel(condition = "input.rowdendlc == 1",
hr(),
h4(strong("Dendrogramma su riga")),
sliderInput("sliderrowheatlc", "Numero cluster:", min = 2, max = 10, value = 2),
),
conditionalPanel(condition = "input.columndendlc == 1",
hr(),
h4(strong("Dendrogramma su colonna")),
uiOutput("slidercolheatlc"),
)
)
), #end of conditionalpanel grafici
# PCA
conditionalPanel(condition = "input.tabboxlcxlc == 'tabpcalc'",
#selectInput("selyearpca", "Seleziona l'anno", choices = "", multiple = FALSE),
selectInput("numcamppcalc", "Scegli il numero di campionamento", choices = "", multiple = FALSE),
awesomeCheckbox("scalepcalc", "Scala i dati", value = TRUE)
)
), #end of sidebarpanel
mainPanel(width=10,
tabBox(id = "tabboxlcxlc", width=NULL,
tabPanel(tagList(shiny::icon("table"), HTML(" Tabella")), value = "tabdtlc",
box(width = NULL, status = "primary", style = "overflow-x: scroll;",
DT::DTOutput("dtlcxlc")),
mod_render_NAbox_ui("naboxlc")
),
### Galleria
tabPanel(tagList(shiny::icon("images"), HTML(" Galleria")), value = "tablccroma",
fluidPage(
fluidRow(
column(4,
fluidRow(
column(6,
box(width = NULL, status = "primary",
radioGroupButtons("ncampcromatlc", "Numero campionamento", choices = c("1" = "1_campionamento", "2" = "2_campionamento"),
individual = TRUE, checkIcon = list(yes = tags$i(class = "fa fa-circle", style = "color: steelblue"), no = tags$i(class = "fa fa-circle-o", style = "color: steelblue")))
)
)
),
fluidRow(column(12, box(width=NULL, status = "primary", style = "overflow-x: scroll;", DT::DTOutput("dtfotolc"))))
),
conditionalPanel(condition = "input.dtfotolc_rows_selected == 0",
p(strong(h4("Per favore seleziona un'azienda dalla tabella", align = "center")))
),
conditionalPanel(condition = "input.dtfotolc_rows_selected != 0",
column(8,
fluidRow(
box(width=NULL, status = "primary", title = "Cromatogramma", align= "center", uiOutput("phcromatlc"))
),
fluidRow(
column(10, offset = 1,
box(width=NULL, status = "primary",title = "Polifenoli",align = "center",
DTOutput("poliffotolc"))
)
)
)
)
) #end of fluidRow
)
), #end of tabpanel Galleria
##### Grafici
tabPanel(tagList(shiny::icon("chart-bar"), HTML(" Grafici")), value = "tabgraphlc",
tabsetPanel(id = "boxlcgraph",
tabPanel("Scatter plot", value = "tabpanscattlc",
shinycssloaders::withSpinner(image = "www/running_olive.gif", plotly::plotlyOutput("scatterlc", height = "550px"))
),
#barplot
tabPanel("Barplot", value = "tabpanbarlc",
shinycssloaders::withSpinner(image = "www/running_olive.gif", plotly::plotlyOutput("barplotlc", height = "550px"))
),
tabPanel("Heatmap", value = "tabpanheatlc",
br(),
InteractiveComplexHeatmap::InteractiveComplexHeatmapOutput("heatmap_lc_output", layout = "1|(2-3)", width1 = 1150, height1 = 700)
)
)
), # end of tabpanel grafici
###### PCA
tabPanel(tagList(shiny::icon("chart-line"), HTML(" PCA")), value = "tabpcalc",
tabsetPanel(
tabPanel("Plot",
br(),
fluidPage(
fluidRow(
column(3,box(width = NULL, status = "primary",
awesomeRadio("selbiplotlc", "Seleziona tipo di grafico", choices = c("Biplot", "Plot"))
)),
column(4, box(width = NULL, status = "primary",
selectInput("colbiplotlc", "Seleziona colonna riempimento", choices = c("Codice_azienda", "Cultivar_principale", "Areale", "Provincia")))),
column(4, box(width = NULL, status = "primary",
awesomeCheckboxGroup("shpbiplotlc", "Aggiungi geometria", choices = "Provincia", inline = TRUE)
))
),
shinycssloaders::withSpinner(image = "www/running_olive.gif", plotly::plotlyOutput("biplotlc", height = "500px")))
),
tabPanel("Screeplot",
br(),
shinycssloaders::withSpinner(image = "www/running_olive.gif", plotly::plotlyOutput("screeplotlc", width = "75%"))
),
tabPanel("Loadings",
br(),
fluidPage(
fluidRow(column(4, box(width = NULL, status = "primary", uiOutput("sliderpclc")))),
shinycssloaders::withSpinner(image = "www/running_olive.gif", plotly::plotlyOutput("loadingslc", height = "550px")))
),
tabPanel("Plot 3D",
br(),
fluidPage(
fluidRow(
column(4, box(width = NULL, status = "primary",
selectInput("col3dlc", "Seleziona colonna riempimento", choices = c("Codice_azienda", "Provincia", "Cultivar_principale", "Areale"))))
),
shinycssloaders::withSpinner(image = "www/running_olive.gif", plotly::plotlyOutput("pca3dlc", height = "500px")))
)
) #end of tabsetpanel
) #end of tabpanel PCA
) #end of tabbox
) #end of mainpanel
)
), #end of tabitem "lcpolsub"
##### Tab morfometria #####
tabItem(tabName = "anmorfosub",
sidebarLayout(
sidebarPanel(width = 2,
radioGroupButtons("selfilemorfo", "Seleziona la morfometria da analizzare",
choiceValues = list("foglie", "drupe", "endocarpo", "rapporti"),
choiceNames = list(
paste(shiny::icon("leaf", style='font-size:16px;'), HTML("<b style=font-size:16px> Foglie</b>")),
paste(tags$img(src = "www/olive_icon2.png", height = "22px", width = "22px"), HTML("<b style=font-size:16px> Drupe</b>")),
paste(tags$img(src = "www/seed_icon2.png", height = "20px", width = "20px"), HTML("<b style=font-size:16px> Endocarpo</b>")),
paste(tags$img(src = "www/ratio_icon2.png", height = "19px", width = "19px"), HTML("<b style=font-size:16px> Rapporti</b>"))),
direction = "vertical", justified = TRUE, status = "primary"
),
hr(),
# Tabella
conditionalPanel(condition = "input.tabboxmorfo == 'tabdtmor'",
h4(strong("Parametri sintesi")),
selectInput("selyeardtmorfo", "Seleziona l'anno", choices = "", multiple = TRUE),
numericInput("selroundmorfo", value = 3,
label = tags$span("Numero di cifre decimali",
tags$i(class = "glyphicon glyphicon-info-sign", style = "color:#0072B2;",
title = "Scegli quante cifre decimali mostrare nella tabella."))
),
hr(),
materialSwitch(inputId = "summarizetab",
label = tags$span(
"Sintetizza i dati",
tags$i(
class = "glyphicon glyphicon-info-sign",
style = "color:#0072B2;",
title = "Attenzione! Sintetizzando i dati verranno perse le informazioni
sulla classificazione IOC."
)),
value = TRUE, status = "primary"),
conditionalPanel(condition = "input.summarizetab == true",
awesomeCheckboxGroup("selectdtmorfo",
label = tags$span(
"Seleziona la colonna da usare per la sintesi",
tags$i(class = "glyphicon glyphicon-info-sign", style = "color:#0072B2;",
title = "La variabile per cui sintetizzare i dati.
Esempio: con 'Codice_azienda' le misure di ogni azienda sono mediate e si avrà una sola riga per ogni azienda,
mentre se si seleziona 'Cultivar_principale' e 'Provincia' la sintesi è eseguita per queste due variabili
e, dunque, si avranno cinque valori per ogni cultivar, uno per provincia (es. Ravece-SA, Ravece-AV...). Aggiungendo
'Anno', le misure tra i vari anni non verranno mediate ma rimarranno separate.")),
choices = c("Codice_azienda", "Provincia", "Azienda", "Cultivar_principale", "Anno"), selected = c("Codice_azienda", "Anno"))
)
),
# Grafici
conditionalPanel(condition = "input.tabboxmorfo == 'tabpanmorfograph'",
h4(strong("Impostazioni grafici")),
#boxplot e barplot
conditionalPanel(
condition = "input.boxmorfograph == 'tabpanboxmorfo' || input.boxmorfograph == 'tabpanbarmorfo'",
selectInput("selectxmorfobb", "Seleziona la colonna X", choices = c("Codice_azienda", "Provincia", "Azienda", "Cultivar_principale"), multiple = FALSE),
selectInput("selectymorfobb", "Seleziona la colonna Y", choices = "", multiple = FALSE),
selectInput("selectfillmorfobb", "Colonna da usare come riempimento", choices = c("Codice_azienda", "Provincia", "Azienda", "Cultivar_principale"), multiple = FALSE)
),
conditionalPanel(
"input.boxmorfograph == 'tabpanbarmorfo'",
checkboxGroupInput("selyearbarmorfo", "Seleziona anno", choices = "")
),
#scatterplot
conditionalPanel(
condition = "input.boxmorfograph == 'tabpanscattmorfo'",
materialSwitch(inputId = "summarizescatt", label = "Sintetizza i dati", value = TRUE, status = "primary"),
conditionalPanel(condition = "input.summarizescatt == true",
selectInput("selectsummscatt", "Seleziona la colonna da usare per la sintesi", choices = c("Codice_azienda", "Provincia", "Azienda", "Cultivar_principale", "Anno"),
selected = c("Codice_azienda","Anno"), multiple = TRUE),
hr(),
),
selectInput("selectxmorfoscatt", "Seleziona la colonna X", choices = "", multiple = FALSE),
selectInput("selectymorfoscatt", "Seleziona la colonna Y", choices = "", multiple = FALSE),
selectInput("selectfillmorfoscatt", "Colonna da usare come riempimento", choices = "", multiple = FALSE)
),
#IOC
conditionalPanel(
condition = "input.boxmorfograph == 'tabpaniocmorfo'",
radioButtons("selplotioc", label = h4("Tipo di grafico"), choices = list("Grafico a torta" = 1, "Grafico a barre" = 2), selected = 2),
selectInput("selectfillmorfoioc", "Misura IOC", choices = "", multiple = FALSE),
conditionalPanel(condition = "input.selplotioc == 2",
selectInput("selectxmorfoioc", "Seleziona la colonna X", choices = c("Codice_azienda", "Provincia", "Azienda", "Cultivar_principale"), multiple = FALSE),
awesomeRadio("iocselfreq", "Frequenza", choices = c("Frequenza assoluta", "Frequenza relativa"))
),
div(actionButton("addiocmorfo2", label = "Aggiungi secondo grafico"), align = "center"),
conditionalPanel(condition = "input.addiocmorfo2 != 0",
br(),
radioButtons("selplotioc2", label = h4("Tipo di grafico"), choices = list("Grafico a torta" = 1, "Grafico a barre" = 2), selected = 2),
selectInput("selectfillmorfoioc2", "Misura IOC", choices = "", multiple = FALSE),
conditionalPanel(condition = "input.selplotioc2 == 2",
selectInput("selectxmorfoioc2", "Seleziona la colonna X", choices = c("Codice_azienda", "Provincia", "Azienda", "Cultivar_principale"), multiple = FALSE),
awesomeRadio("iocselfreq2", "Frequenza", choices = c("Frequenza assoluta", "Frequenza relativa"))
)
)
),
# HEATMAP
conditionalPanel(
condition = "input.boxmorfograph == 'tabpanheatmorfo'",
div(actionButton("updateheatmorfo", label = "Carica!", class = "btn btn-primary btn-lg", width = "140px", style='padding:5px; font-size:150%; font-weight: bold;'), align= "center"),
br(),
h4(strong("Dati")),
selectInput("numheatmorfo", "Scegli il numero di campionamento", choices = "", multiple = FALSE),
selectInput("selyearheatmorfo", "Seleziona l'anno", choices = "", multiple = FALSE),
hr(),
h4(strong("Opzioni dendrogramma")),
###voglio il dendrograma su riga o colonna o entrambi?
h5(strong("Scegli dove mostrare il dendrogramma")),
fluidRow(
column(6, materialSwitch(inputId = "rowdendmorfo", label = "Riga", value = TRUE, status = "primary", width = "90%")),
column(6, materialSwitch(inputId = "columndendmorfo", label = "Colonna", value = TRUE, status = "primary", width = "90%"))
),
selectInput("selectannotmorfo", "Colonna annotazione:", choices = c("Provincia", "Cultivar_principale")),
conditionalPanel(condition = "input.rowdendmorfo == 1 || input.columndendmorfo == 1",
selectInput("seldistheatmorfo", "Funzione di distanza:", choices = c("euclidean", "maximum", "manhattan", "canberra", "minkowski"), selected = "euclidean"),
selectInput("selhclustheatmorfo", "Metodo clustering:", choices = c("ward.D", "ward.D2", "single", "complete", "average" , "mcquitty", "median", "centroid"), selected = "complete"),
),
conditionalPanel(condition = "input.rowdendmorfo == 0",
h5(strong("Ordinare i dati per annotazione?")),
awesomeCheckbox("heatsortmorfo", label = "Ordina", value = TRUE)
),
conditionalPanel(condition = "input.rowdendmorfo == 1",
hr(),
h4(strong("Dendrogramma su riga")),
sliderInput("sliderrowheatmorfo", "Numero cluster:", min = 2, max = 10, value = 2),
),
conditionalPanel(condition = "input.columndendmorfo == 1",
hr(),
h4(strong("Dendrogramma su colonna")),
uiOutput("sliderheatcolmorfo"),
)
),
conditionalPanel(condition = "input.boxmorfograph == 'tabpancorrmorfo'",
selectInput("selyearcorrmorfo", "Seleziona l'anno", choices = "", multiple = FALSE)
)
), #end of conditionapanel dei grafici
# PCA
conditionalPanel(
condition = "input.tabboxmorfo == 'tabpcamor'",
selectInput("selyearpcamorfo", "Seleziona l'anno", choices = "", multiple = FALSE),
selectInput("numpcamorfo", "Scegli il numero di campionamento", choices = "", multiple = FALSE),
materialSwitch(inputId = "summarizepcamorfo", label = "Sintetizza i dati", value = TRUE, status = "primary"),
radioGroupButtons(inputId = "selcorpcamorfo", label = "Matrice:", choices = c("Correlazione" = TRUE, "Covarianza" = FALSE),
individual = TRUE, checkIcon = list(yes = tags$i(class = "fa fa-circle", style = "color: steelblue"),no = tags$i(class = "fa fa-circle-o", style = "color: steelblue")))
),
# Clustering
conditionalPanel(
condition = "input.tabboxmorfo == 'tabclustmor'",
selectInput("selcolclustmorfo", "Seleziona variabile", choices = c("Codice_azienda", "Cultivar_principale")),
selectInput("selyearclustmorfo", "Seleziona l'anno", choices = "", multiple = TRUE),
selectInput("numclustmorfo", "Scegli il numero di campionamento", choices = "", multiple = FALSE),
#materialSwitch(inputId = "summarizeclustmorfo", label = "Sintetizza i dati", status = "primary", value = TRUE),
radioGroupButtons("selclustmethod", "Tipo di clustering", choices = c("Gerarchico", "Partizionale"), justified = TRUE, status = "primary"),
conditionalPanel(
condition = "input.selclustmethod == 'Partizionale'",
selectInput("selclusthmorfo", "Seleziona l'algoritmo di clustering", choices = c("K-means", "PAM", "Clara"), selected = "K-means", multiple = FALSE),
)
),
#Test d'ipotesi
conditionalPanel(condition = "input.tabboxmorfo == 'tabpanmorfotest'",
h4(strong("Opzioni test")),
selectInput("selyearttestmorfo", "Scegli l'anno", choices = "", multiple = TRUE),
hr(),
#T-test
conditionalPanel(condition = "input.boxmorfotest == 'tabpanttestmorfo'",
selectInput("catvarttest", "Variabile categorica", choices = "", multiple = FALSE),
selectInput("culttest1", "Variabile dipendente", choices = "", multiple = FALSE),
selectInput("culttest2", "Fattore esplicativo", choices = "", multiple = FALSE),
selectInput("numvarttest", "Variabile numerica da confrontare", choices = "", multiple = FALSE),
awesomeRadio("selectttest", "Tipo di test", choices = c("T-test", "Wilcoxon-Mann-Whitney")),
conditionalPanel(condition = "input.selectttest == 'T-test'",
awesomeCheckbox("selvarequal", "Omoschedasticità", value = TRUE)
)
),
#Test correlazione
conditionalPanel(
condition = "input.boxmorfotest == 'tabpancorrtestmorfo'",
selectInput("corrtest1", "Variabile dipendente", choices = "", multiple = FALSE),
selectInput("corrtest2", "Fattore esplicativo", choices = "", multiple = FALSE),
awesomeRadio("selectcorrtest", "Tipo di test", choices = c("Pearson" = "pearson", "Kendall" = "kendall", "Spearman" = "spearman")),
hr(),
selectInput("corrtestfill", "Colonna riempimento", choices = "", multiple = FALSE),
awesomeCheckbox("numfitcorrtest", "Singolo fit", value = TRUE),
awesomeCheckbox("selsecorrtest", "Intervallo di confidenza", value = TRUE),
),
#Test indipendenza
conditionalPanel(
condition = "input.boxmorfotest == 'tabpanchisqtestmorfo'",
selectInput("chisqtest1", "Variabile descrittiva", choices = c("Codice_azienda", "Provincia", "Cultivar_principale"), multiple = FALSE, selected = "Cultivar_principale"),
selectInput("chisqtest2", "Variabile categorica", choices = "", multiple = FALSE),
awesomeRadio("selectchisqtest", "Tipo di test", choices = c("Test esatto di Fisher", "Test d'indipendenza Chi-quadro")),
awesomeCheckbox("simulatechisq", "Simulazione p-value (Monte Carlo)", value = TRUE),
awesomeRadio("pvalchisqmorfo", "Livello di significatività", choices = c(0.01, 0.05, 0.1), selected = 0.05),
selectInput("chisqtestfilt", "Filtrare i dati (opzionale)", choices = "", multiple = TRUE)
),
#Test Anova
conditionalPanel(condition = "input.boxmorfotest == 'tabpananovamorfo'",
awesomeRadio("selectanovatest", "Tipo di test", choices = c("One-way ANOVA", "Two-way ANOVA")),
conditionalPanel(condition = "input.selectanovatest == 'One-way ANOVA'",
awesomeRadio("selectanovatest2", "Tipo di test", choices = c("ANOVA", "Kruskal-Wallis")),
),
awesomeRadio("pvalanovamorfo", "Livello di significatività", choices = c(0.01, 0.05, 0.1), selected = 0.05),
selectInput("anovanum", "Variabile numerica", choices = "", multiple = FALSE),
selectInput("anovacat", "Variabile categorica", choices = "", multiple = FALSE),
conditionalPanel(condition = "input.selectanovatest == 'Two-way ANOVA'",
selectInput("anovacat2", "Seconda variabile categorica", choices = "", multiple = FALSE),
awesomeRadio("anova2typemorfo", "Tipo di ANOVA", choices = c("Modello additivo", "Modello con interazione"))
)
),
),
# Mappa
conditionalPanel(
condition = "input.tabboxmorfo == 'tabmapmor'",
div(actionButton("upmapmorfo", "Carica mappa", class = "btn-primary", style = 'padding:4px; font-size:160%'), align = "center"),
conditionalPanel(
condition = ("input.upmapmorfo != 0"),
br(),
selectInput("mapxmorfomap1", "Seleziona la colonna da visualizzare", choices = "", multiple = FALSE),
selectInput("selyearmorfomap1", "Seleziona l'anno", choices = "", multiple = FALSE),
selectInput("nummorfomap1", "Scegli il numero di campionamento", choices = "", multiple = FALSE),
div(actionButton("addmapmorfo2", label = "Aggiungi seconda mappa"), align = "center"),
conditionalPanel(
condition = ("input.addmapmorfo2 != 0"),
br(),
selectInput("mapxmorfomap2", "Seleziona la colonna da visualizzare", choices = "", multiple = FALSE),
selectInput("selyearmorfomap2", "Seleziona l'anno", choices = "", multiple = FALSE),
selectInput("nummorfomap2", "Scegli il numero di campionamento", choices = "", multiple = FALSE)
)
)
)
), #end of sidebarpanel
#### mainpanel ####
mainPanel(width = 10,
tabBox(id = "tabboxmorfo", width=NULL,
tabPanel(tagList(shiny::icon("table"), HTML(" Tabella")), value = "tabdtmor",
fluidPage(
fluidRow(box(width = 12, status = "primary", style = "overflow-x: scroll;",
DT::DTOutput("dtmorfo"))),
mod_render_NAbox_ui("naboxmorfo")
)
),
tabPanel(tagList(shiny::icon("images"), HTML(" Galleria")), value = "tabmorfomor",
fluidPage(
fluidRow(
column(width=4,
fluidRow(
column(6, box(width = NULL, status = "primary",
radioGroupButtons(
inputId = "campfotomorfo", label = "Numero campionamento",
choices = c("1" = "1_campionamento", "2" = "2_campionamento"), individual = TRUE,
checkIcon = list(yes = tags$i(class = "fa fa-circle", style = "color: steelblue"),
no = tags$i(class = "fa fa-circle-o", style = "color: steelblue"))
))
),
column(6, box(width=NULL, status = "primary",
selectInput("selyearfotomorfo", "Seleziona l'anno", choices = "", multiple = FALSE))
)
),
fluidRow(column(12, box(width=NULL, status = "primary", style = "overflow-x: scroll;", DT::DTOutput("dtfotomorfo"))))
),
column(width = 8,
column(width = 6, offset = 3,
conditionalPanel(condition = "input.dtfotomorfo_rows_selected == 0",
box(width = NULL, background = "yellow", tags$i(class = "fas fa-exclamation-triangle", style="font-size: 27px"), h4(strong("Seleziona un'azienda dalla tabella"), style = "color: white"), style = "text-align: justify; text-align: center;"),
),
conditionalPanel(condition = "input.dtfotomorfo_rows_selected != 0 && input.campfotomorfo == '1_campionamento'",
box(width = NULL, background = "yellow", tags$i(class = "fas fa-exclamation-triangle", style="font-size: 27px"), h4(strong("Nessuna foto in archivio. I dati sulla morfometria riguardano solamente il secondo campionamento."), style = "color: white"), style = "text-align: justify; text-align: center;"),
)
),
conditionalPanel(
condition = "input.dtfotomorfo_rows_selected != 0 && input.campfotomorfo == '2_campionamento'",
uiOutput("phmorfo")
)
)
) #end of fluidRow
)
), #end of tabpanel Foto
tabPanel(tagList(shiny::icon("chart-bar"), HTML(" Grafici")), value = "tabpanmorfograph",
tabsetPanel(id = "boxmorfograph",
tabPanel("Boxplot", value = "tabpanboxmorfo",
shinycssloaders::withSpinner(image = "www/running_olive.gif", plotly::plotlyOutput("boxmorfo"))
),
tabPanel("Barplot", value = "tabpanbarmorfo",
shinycssloaders::withSpinner(image = "www/running_olive.gif", plotly::plotlyOutput("barmorfo"))
),
tabPanel("Scatter plot", value = "tabpanscattmorfo",
shinycssloaders::withSpinner(image = "www/running_olive.gif", plotly::plotlyOutput("scattmorfo"))
),
tabPanel("IOC", value = "tabpaniocmorfo",
shinycssloaders::withSpinner(image = "www/running_olive.gif", plotly::plotlyOutput("iocmorfo")),
conditionalPanel(condition = "input.addiocmorfo2 != 0",
hr(),
shinycssloaders::withSpinner(image = "www/running_olive.gif", plotly::plotlyOutput("iocmorfo2")),
)
),
tabPanel("Heatmap", value = "tabpanheatmorfo",
br(),
InteractiveComplexHeatmap::InteractiveComplexHeatmapOutput("heatmap_morfo_output", layout = "1|(2-3)", width1 = 850, height1 = 600)
),
tabPanel("Correlation plot", value = "tabpancorrmorfo",
br(),
shinycssloaders::withSpinner(image = "www/running_olive.gif", plotly::plotlyOutput("corrplotmorfo"))
)
)
),
#pca
tabPanel(tagList(shiny::icon("chart-line"), HTML(" PCA")), value = "tabpcamor",
tabsetPanel(
tabPanel("Plot",
br(),
fluidPage(
fluidRow(
column(3, box(width = NULL, status = "primary",
awesomeRadio("selbiplotmorfo", "Seleziona tipo di grafico", choices = c("Biplot", "Plot")))),
column(3, box(width = NULL, status = "primary",
selectInput("colbiplotmorfo", "Seleziona colonna riempimento", choices = c("Codice_azienda", "Provincia", "Cultivar_principale", "Areale")))),
column(3, box(width = NULL, status = "primary",
awesomeCheckboxGroup(inputId = "shpbiplotmorfo", label = "Aggiungi geometria", choices = "Provincia", inline = TRUE)
))
),
shinycssloaders::withSpinner(image = "www/running_olive.gif", plotly::plotlyOutput("biplotmorfo", height = "500px")))
),
tabPanel("Screeplot",
br(),
shinycssloaders::withSpinner(image = "www/running_olive.gif", plotly::plotlyOutput("screeplotmorfo", width = "75%"))
),
tabPanel("Loadings",
br(),
fluidPage(
fluidRow(column(4, box(width = NULL, status = "primary",
uiOutput("sliderpcmorfo")))),
shinycssloaders::withSpinner(image = "www/running_olive.gif", plotly::plotlyOutput("loadingsmorfo")))
),
tabPanel("Plot 3D",
br(),
fluidPage(
fluidRow(
column(4, box(width = NULL, status = "primary",
selectInput("col3dmorfo", "Seleziona colonna riempimento", choices = c("Codice_azienda", "Provincia", "Cultivar_principale", "Areale"))))
),
shinycssloaders::withSpinner(image = "www/running_olive.gif", plotly::plotlyOutput("pca3dmorfo", height = "500px")))
)
)
), #end of tabpanel PCA
# Clustering
tabPanel(tagList(tags$img(src = "www/clustering_icon.png", height = "16px", width = "16px"), HTML(" Clustering")), value = "tabclustmor",
tabsetPanel(
tabPanel("Cluster plot",
br(),
fluidPage(
fluidRow(
column(4,
box(width = NULL, status = "primary",
sliderInput("selnumclustmorfo", "Numero cluster:", min = 1, max = 10, value = 2))),
column(4,
conditionalPanel(condition = "input.selclustmethod == 'Gerarchico'",
box(width=NULL, status = "primary",
selectInput("selhclustmeth", "Seleziona metodo agglomerazione", choices = c("single", "complete", "ward.D", "ward.D2"), selected = "ward.D2"))
)
)
),
shinycssloaders::withSpinner(image = "www/running_olive.gif", plotOutput("plotclustermorfo", height = "600px"))
)
),
tabPanel("Numero cluster",
br(),
shinycssloaders::withSpinner(image = "www/running_olive.gif", plotOutput("numclustergraph", height = "800px"))
)
)
), #end of tabpanel clustering
#tabpanel test d'ipotesi
tabPanel(tagList(shiny::icon("clipboard-check"), HTML(" Test d'ipotesi")), value = "tabpanmorfotest",
tabsetPanel(id = "boxmorfotest",
# Test di correlazione
tabPanel("Test di correlazione", value = "tabpancorrtestmorfo",
br(),
fluidPage(
fluidRow(
column(6, box(width = NULL, title = strong("Test sulla normalità"), status = "primary", verbatimTextOutput("shapirocorr1"))),
column(6, box(width = NULL, title = strong("Test sulla normalità"), status = "primary", verbatimTextOutput("shapirocorr2")))
),
fluidRow(
column(6,
conditionalPanel(condition = "input.corrtest1 != input.corrtest2",
box(width = NULL, title = strong("Test statistico"), status = "primary", verbatimTextOutput("corrtest"))),
conditionalPanel(condition = "input.corrtest1 == input.corrtest2",
box(width = NULL, title = strong("Test statistico"), status = "warning", tags$i(class = "fas fa-exclamation-triangle", style="font-size: 20px; color: rgb(243,156,18)"),
h5(strong("Errore. La variabile dipendente e il fattore esplicativo devono essere diversi.", style = "color: rgb(243,156,18)")), style = "text-align: justify; text-align: center;"))
),
column(6, box(width = NULL, title = strong("Grafico"), status = "primary",
shinycssloaders::withSpinner(image = "www/running_olive.gif", plotly::plotlyOutput("scattcorrtest"))))
)
),
), #end of tabpanel
tabPanel("Confronto tra due gruppi", value = "tabpanttestmorfo",
br(),
fluidPage(
fluidRow(
column(6, box(width = NULL, title = strong("Test sulla normalità"), status = "primary", verbatimTextOutput("shapiro1"))),
column(6, box(width = NULL, title = strong("Test sulla normalità"), status = "primary", verbatimTextOutput("shapiro2")))
),
fluidRow(
conditionalPanel(condition = "input.culttest1 != input.culttest2 && (output.shapttestmorfoui == 'distribuzione normale' || input.selectttest == 'Wilcoxon-Mann-Whitney')",
column(6,box(width = NULL, title = strong("Test sulla varianza"), status = "primary", verbatimTextOutput("vartest1"))),
column(6,box(width = NULL, title = strong("Test statistico"), status = "primary", verbatimTextOutput("ttest1")))
),
conditionalPanel(condition = "input.culttest1 == input.culttest2",
column(6, box(width = NULL, title = strong("Test sulla varianza"), status = "warning", tags$i(class = "fas fa-exclamation-triangle", style="font-size: 20px; color: rgb(243,156,18)"),
h5(strong("Errore. La variabile dipendente e il fattore esplicativo devono essere diversi.", style = "color: rgb(243,156,18)")), style = "text-align: justify; text-align: center;")),
column(6, box(width = NULL, title = strong("Test statistico"), status = "warning", tags$i(class = "fas fa-exclamation-triangle", style="font-size: 20px; color: rgb(243,156,18)"),
h5(strong("Errore. La variabile dipendente e il fattore esplicativo devono essere diversi.", style = "color: rgb(243,156,18)")), style = "text-align: justify; text-align: center;"))
),
conditionalPanel(
condition = "input.culttest1 != input.culttest2 && output.shapttestmorfoui == 'distribuzione non normale' && input.selectttest == 'T-test'",
column(6, offset = 3,
box(width = NULL, status = "warning", style = "text-align: justify; text-align: center;", br(),
tags$i(class = "fas fa-exclamation-triangle", style="font-size: 25px; color: rgb(243,156,18)"),
h4(strong("Una o più variabili non seguono una distribuzione normale. Scegli il Wilcoxon-Mann-Whitney test.", style = "color: rgb(243,156,18)")),
br()
)
)
)
),
fluidRow(
column(8, offset = 2, box(width = NULL, title = strong("Grafico"), status = "primary",
shinycssloaders::withSpinner(image = "www/running_olive.gif", plotly::plotlyOutput("boxttest"))))
)
) #end of fluidpage
), #end of tabpanel conf 2 gruppi
# Confronto tra più gruppi
tabPanel("Confronto tra più gruppi", value = "tabpananovamorfo",
fluidPage(
fluidRow(
column(12, box(width = NULL, title = strong("Boxplot"), status = "primary",
shinycssloaders::withSpinner(image = "www/running_olive.gif", plotly::plotlyOutput("boxanova"))))
),
fluidRow(
column(6, box(width = NULL, title = strong("Test sulla normalità"), status = "primary", verbatimTextOutput("shapiroanova1"))),
conditionalPanel(condition = "(output.shapanovamorfoui == 'distribuzione normale' && (input.selectanovatest2 == 'ANOVA' || input.selectanovatest2 == 'Kruskal-Wallis')) || (output.shapanovamorfoui == 'distribuzione non normale' && input.selectanovatest2 == 'Kruskal-Wallis')",
conditionalPanel(condition = "input.selectanovatest2 == 'ANOVA'",
column(6, box(width = NULL, title = strong("Test ANOVA"), status = "primary", verbatimTextOutput("anova1morfoprint")))
),
conditionalPanel(condition = "input.selectanovatest2 == 'Kruskal-Wallis'",
column(6, box(width = NULL, title = strong("Test Kruskal-Wallis"), status = "primary", verbatimTextOutput("kruskmorfo")))
)
),
conditionalPanel(condition = "output.shapanovamorfoui == 'distribuzione non normale' && input.selectanovatest2 == 'ANOVA'",
column(6, box(width = NULL, title = strong("Test ANOVA"), status = "warning", style = "text-align: justify; text-align: center;",
tags$i(class = "fas fa-exclamation-triangle", style="font-size: 25px; color: rgb(243,156,18)"),
h4(strong("La variabile numerica non segue la distribuzione normale. Scegli il test Kruskal-Wallis.", style = "color: rgb(243,156,18)")),
))
)
),
conditionalPanel(condition = "(output.shapanovamorfoui == 'distribuzione normale' && (input.selectanovatest2 == 'ANOVA' || input.selectanovatest2 == 'Kruskal-Wallis')) || (output.shapanovamorfoui == 'distribuzione non normale' && input.selectanovatest2 == 'Kruskal-Wallis')",
fluidRow(
column(10,offset = 1,
box(width = NULL, title = strong("Post-hoc"), status = "primary", style = "text-align: justify; text-align: center;",
conditionalPanel(condition = "output.signiftestmorfoui == 'significativo'",
conditionalPanel(condition = "input.selectanovatest2 == 'ANOVA'",
h4(strong("Tukey HSD"))),
conditionalPanel(condition = "input.selectanovatest2 == 'Kruskal-Wallis'",
h4(strong("Dunn Test")),
),
shinycssloaders::withSpinner(image = "www/running_olive.gif", plotly::plotlyOutput("posthocmorfograph"))
),
conditionalPanel(condition = "output.signiftestmorfoui == 'non significativo'",
tags$i(class = "fas fa-exclamation-triangle", style="font-size: 25px; color: rgb(243,156,18)"),
h4(strong("Il p-value è maggiore del livello di significatività impostato. Non ci sono differenze significative tra le variabili.", style = "color: rgb(243,156,18)"))
)
)
)
) #end of fluidrow post-hoc
)
) #end of fluidpage
), #end of tabpanel più gruppi
#Test d'indipendenza
tabPanel("Test d'indipendenza", value = "tabpanchisqtestmorfo",
br(),
fluidPage(
fluidRow(
column(5, box(width = NULL, title = strong("Tabella di contingenza"), status = "primary", tableOutput("contingtablemorfo"))),
column(6,
fluidRow(
box(width = NULL, title = strong("Test"), status = "primary", verbatimTextOutput("chisqmorfoprint"))
),
fluidRow(
conditionalPanel(condition = "output.signiftestchisqmorfoui == 'significativo'",
#box(width = NULL, title = strong("Grafico residui"), status = "primary", style = "text-align: justify; text-align: center;",
shinycssloaders::withSpinner(image = "www/running_olive.gif", plotOutput("plotresidchisq"))
# )
),
conditionalPanel(condition = "output.signiftestchisqmorfoui == 'non significativo'",
box(width = NULL, status = "warning", style = "text-align: justify; text-align: center;",
tags$i(class = "fas fa-exclamation-triangle", style="font-size: 25px; color: rgb(243,156,18)"),
h4(strong("Il p-value è maggiore del livello di significatività impostato. Le variabili sono indipendenti.", style = "color: rgb(243,156,18)"))
)
)
) #end of fluidrow grafico
)
) #end of first fluidrow
)
)
) #end of tabset panel
),
#tabpanel mappa
tabPanel(tagList(shiny::icon("map-marked-alt"), HTML(" Mappa")), value = "tabmapmor",
conditionalPanel(condition = ("input.upmapmorfo != 0"),
shinycssloaders::withSpinner(tmapOutput("mapmorfo1")),
conditionalPanel(condition = "input.addmapmorfo2 != 0",
hr(),
shinycssloaders::withSpinner(tmapOutput("mapmorfo2"))
)
))
) #end of tabBox
) #end of mainpanel
) #end of sidebarlayout
), #end of tabitem morfo
##### Tab integrazione dati ####
tabItem(
tabName = "integrdati",
sidebarLayout(
sidebarPanel(
width = 2,
h4(strong("Scegli un confronto")),
radioGroupButtons("conf_type1", "Scegli una prima variabile",
choiceValues = list("tot","ind"),
choiceNames = list(
paste(icon("circle"), HTML("<b> Polifenoli totali</b>")),
paste(icon("circle"), HTML("<b> Polifenoli individuali</b>"))
),direction = "vertical", justified = TRUE, status = "primary"),
radioGroupButtons("conf_type2", "Scegli una seconda variabile",
choiceValues = list("camp", "prec", "ind"),
choiceNames = list(
paste(icon("circle"), HTML("<b> Schede campionamento</b>")),
paste(icon("circle"), HTML("<b> Precipitazioni</b>")),
paste(icon("circle"), HTML("<b> Polifenoli individuali</b>"))
),direction = "vertical", justified = TRUE, status = "primary"),
hr(),
selectInput("conf_selpoltot", "Seleziona una misura", choices = c("Foglie", "Drupe", "Olio", "Posa", "Sansa")),
conditionalPanel(
condition = "input.conf_type2 == 'prec'",
selectInput("varmeteo_conf", "Seleziona misura di precipitazione", choices = c("Precipitazioni totali" = "tp",
"Volume d'acqua nel suolo (7-28cm)" = "swvl2",
"Volume d'acqua nel suolo (28-100cm)" = "swvl3"))
),
selectInput("conf_selyear", "Scegli uno o più anni", choices = c("2020", "2021"), multiple = TRUE, selected = "2020"),
conditionalPanel(
condition = "input.tabboxconf == 'tabpan_testconf'",
selectInput("conf_selcamp_test", "Scegli uno o più campionamenti", choices = "", multiple = TRUE)
),
hr(),
#grafici
conditionalPanel(
condition = "input.tabboxconf == 'tabpan_graphconf' && input.boxconfgraph == 'tabgraph_scattconf'",
h4(strong("Impostazioni grafici")),
awesomeRadio("typescatt_conf", "Dati da analizzare", choices = c("Tutti", "Filtra per cultivar")),
conditionalPanel(
condition = "input.typescatt_conf == 'Filtra per cultivar'",
selectInput("selcult_scatt_conf", "Scegli la/le cultivar", choices = "", multiple = TRUE)),
selectInput("scattx_conf", "Seleziona la colonna X", choices = ""),
selectInput("scatty_conf", "Seleziona la colonna Y", choices = ""),
hr(),
h4(strong("Altre opzioni")),
conditionalPanel(
condition = "input.conf_selyear.length > 1",
awesomeCheckbox("scattfacet_conf", "Dividi gli anni in due grafici", value = FALSE)
),
conditionalPanel(
condition = "input.typescatt_conf == 'Filtra per cultivar'",
awesomeCheckbox("scatt_dens_conf", "Density plot 2D", value = FALSE),
fluidRow(
column(4, br(), awesomeCheckbox("scatt_fit_conf", "Fit", value = FALSE)),
conditionalPanel(
condition = "input.scatt_fit_conf == true",
column(8, awesomeRadio("scatt_selmodfit_conf", "Modello fit", choices = c("lm", "loess"),inline = T))
))
)
),
#### TEST d'ipotesi
#Test d'ipotesi
conditionalPanel(
condition = "input.tabboxconf == 'tabpan_testconf'",
h4(strong("Opzioni test")),
#Test correlazione
conditionalPanel(
condition = "input.boxconftest == 'tabpancorrtest_conf'",
selectInput("corrtest1_conf", "Variabile dipendente", choices = "", multiple = FALSE),
selectInput("corrtest2_conf", "Fattore esplicativo", choices = "", multiple = FALSE),
awesomeRadio("selectcorrtest_conf", "Tipo di test", choices = c("Pearson" = "pearson", "Kendall" = "kendall", "Spearman" = "spearman")),
hr(),
selectInput("corrtestfill_conf", "Colonna riempimento", choices = "", multiple = FALSE),
awesomeCheckbox("numfitcorrtest_conf", "Singolo fit", value = TRUE),
awesomeCheckbox("selsecorrtest_conf", "Intervallo di confidenza", value = TRUE),
awesomeRadio("selmod_fit_conf", "Seleziona un metodo per il fit", choices = c("lm", "loess", "auto"))
),
#T-test
conditionalPanel(
condition = "input.boxconftest == 'tabpanttest_conf'",
selectInput("catvarttest_conf", "Variabile categorica", choices = "", multiple = FALSE),
selectInput("culttest1_conf", "Variabile dipendente", choices = "", multiple = FALSE),
selectInput("culttest2_conf", "Fattore esplicativo", choices = "", multiple = FALSE),
selectInput("numvarttest_conf", "Variabile numerica da confrontare", choices = "", multiple = FALSE),
awesomeRadio("selectttest_conf", "Tipo di test", choices = c("T-test", "Wilcoxon-Mann-Whitney")),
conditionalPanel(condition = "input.selectttest_conf == 'T-test'",
awesomeCheckbox("selvarequal_conf", "Omoschedasticità", value = TRUE)
)
),
#Test Anova
conditionalPanel(
condition = "input.boxconftest == 'tabpananova_conf'",
awesomeRadio("selectanovatest_conf", "Tipo di test", choices = c("One-way ANOVA", "Two-way ANOVA")),
conditionalPanel(
condition = "input.selectanovatest_conf == 'One-way ANOVA'",
awesomeRadio("selectanovatest2_conf", "Tipo di test", choices = c("ANOVA", "Kruskal-Wallis")),
),
awesomeRadio("pvalanovamorfo_conf", "Livello di significatività", choices = c(0.01, 0.05, 0.1), selected = 0.05),
selectInput("anovanum_conf", "Variabile numerica", choices = "", multiple = FALSE),
selectInput("anovacat_conf", "Variabile categorica", choices = "", multiple = FALSE),
conditionalPanel(condition = "input.selectanovatest_conf == 'Two-way ANOVA'",
selectInput("anovacat2_conf", "Seconda variabile categorica", choices = "", multiple = FALSE),
awesomeRadio("anova2typemorfo_conf", "Tipo di ANOVA", choices = c("Modello additivo", "Modello con interazione"))
)
)
#
# #Test indipendenza
# conditionalPanel(
# condition = "input.boxmorfotest == 'tabpanchisqtestmorfo'",
# selectInput("chisqtest1", "Variabile descrittiva", choices = c("Codice_azienda", "Provincia", "Cultivar_principale"), multiple = FALSE, selected = "Cultivar_principale"),
# selectInput("chisqtest2", "Variabile categorica", choices = "", multiple = FALSE),
# awesomeRadio("selectchisqtest", "Tipo di test", choices = c("Test esatto di Fisher", "Test d'indipendenza Chi-quadro")),
# awesomeCheckbox("simulatechisq", "Simulazione p-value (Monte Carlo)", value = TRUE),
# awesomeRadio("pvalchisqmorfo", "Livello di significatività", choices = c(0.01, 0.05, 0.1), selected = 0.05),
# selectInput("chisqtestfilt", "Filtrare i dati (opzionale)", choices = "", multiple = TRUE)
#
#
# ),
#
)
),
mainPanel(width = 10,
tabBox(id = "tabboxconf", width = NULL,
###tabella
tabPanel(tagList(icon("table"), HTML(" Tabella")), value = "tabpan_tableconf",
fluidPage(box(width=12, status = "primary", style = "overflow-x: scroll;", DT::DTOutput("dt_conf"))),
downloadButton("down_integrazione", "Download dati")
),
##### confronti grafici ####
tabPanel(
tagList(icon("chart-bar"), HTML(" Grafici")), value = "tabpan_graphconf",
tabsetPanel(
id = "boxconfgraph",
tabPanel(
"Scatter plot", value = "tabgraph_scattconf",
fluidPage(
box(width=NULL, status = "primary",
fluidRow(
column(3, selectInput("scattnum_conf", "Scegli il numero di campionamento", choices = "", multiple = TRUE)),
column(3, selectInput("scattfill_conf", "Colonna da usare come riempimento", choices = "", multiple = FALSE)),
column(3, selectInput("scattsize_conf", "Colonna da usare come dimensione", choices = "")),
column(3, selectInput("scattshape_conf", "Colonna da usare come forma", choices = ""))
)),
plotly::plotlyOutput("scatterconf",height = "100%"),
)
),
tabPanel(
"Correlation plot", value = "tabgraph_corrconf",
fluidPage(
box(width=NULL, status = "primary",
fluidRow(
column(3, selectInput("corrnum_conf", "Scegli il numero di campionamento", choices = "", multiple = TRUE)),
)),
plotly::plotlyOutput("corrplotconf")
)
)
) #end tabset boxconfgraph
), #end of tabpanel grafici
#####mainpanel test d'ipotesi
#tabpanel test d'ipotesi
tabPanel(
tagList(
icon("clipboard-check"), HTML(" Test d'ipotesi")), value = "tabpan_testconf",
tabsetPanel(
id = "boxconftest",
# Test di correlazione
tabPanel(
"Test di correlazione", value = "tabpancorrtest_conf",
conditionalPanel(
condition = "input.conf_type2 == 'camp'",
br(),
fluidPage(helpText("Test di correlazione non disponibile per questo tipo di confronto"))
),
conditionalPanel(
condition = "input.conf_type2 != 'camp'",
br(),
fluidPage(
fluidRow(
column(6, box(width = NULL, title = strong("Test sulla normalità"), status = "primary", verbatimTextOutput("shapirocorr1_conf"))),
column(6, box(width = NULL, title = strong("Test sulla normalità"), status = "primary", verbatimTextOutput("shapirocorr2_conf")))
),
fluidRow(
column(
6,
conditionalPanel(condition = "input.corrtest1_conf != input.corrtest2_conf",
box(width = NULL, title = strong("Test statistico"), status = "primary", verbatimTextOutput("corrtest_conf"))),
conditionalPanel(condition = "input.corrtest1_conf == input.corrtest2_conf",
box(width = NULL, title = strong("Test statistico"), status = "warning", tags$i(class = "fas fa-exclamation-triangle", style="font-size: 20px; color: rgb(243,156,18)"),
h5(strong("Errore. La variabile dipendente e il fattore esplicativo devono essere diversi.", style = "color: rgb(243,156,18)")), style = "text-align: justify; text-align: center;"))
),
column(6, box(width = NULL, title = strong("Grafico"), status = "primary",
shinycssloaders::withSpinner(image = "www/running_olive.gif", plotly::plotlyOutput("scattcorrtest_conf"))))
)
)
)
), #end of tabpanel
tabPanel(
"Confronto tra due gruppi", value = "tabpanttest_conf",
br(),
fluidPage(
fluidRow(
column(6, box(width = NULL, title = strong("Test sulla normalità"), status = "primary", verbatimTextOutput("shapiro1_conf"))),
column(6, box(width = NULL, title = strong("Test sulla normalità"), status = "primary", verbatimTextOutput("shapiro2_conf")))
),
fluidRow(
conditionalPanel(
condition = "input.culttest1_conf != input.culttest2_conf && (output.shapttestmorfoui_conf == 'distribuzione normale' || input.selectttest_conf == 'Wilcoxon-Mann-Whitney')",
column(6,box(width = NULL, title = strong("Test sulla varianza"), status = "primary", verbatimTextOutput("vartest1_conf"))),
column(6,box(width = NULL, title = strong("Test statistico"), status = "primary", verbatimTextOutput("ttest1_conf")))
),
conditionalPanel(
condition = "input.culttest1_conf == input.culttest2_conf",
column(6, box(width = NULL, title = strong("Test sulla varianza"), status = "warning", tags$i(class = "fas fa-exclamation-triangle", style="font-size: 20px; color: rgb(243,156,18)"),
h5(strong("Errore. La variabile dipendente e il fattore esplicativo devono essere diversi.", style = "color: rgb(243,156,18)")), style = "text-align: justify; text-align: center;")),
column(6, box(width = NULL, title = strong("Test statistico"), status = "warning", tags$i(class = "fas fa-exclamation-triangle", style="font-size: 20px; color: rgb(243,156,18)"),
h5(strong("Errore. La variabile dipendente e il fattore esplicativo devono essere diversi.", style = "color: rgb(243,156,18)")), style = "text-align: justify; text-align: center;"))
),
conditionalPanel(
condition = "input.culttest1_conf != input.culttest2_conf && output.shapttestmorfoui_conf == 'distribuzione non normale' && input.selectttest_conf == 'T-test'",
column(6, offset = 3,
box(width = NULL, status = "warning", style = "text-align: justify; text-align: center;", br(),
tags$i(class = "fas fa-exclamation-triangle", style="font-size: 25px; color: rgb(243,156,18)"),
h4(strong("Una o più variabili non seguono una distribuzione normale. Scegli il Wilcoxon-Mann-Whitney test.", style = "color: rgb(243,156,18)")),
br()
)
)
)
),
fluidRow(
column(8, offset = 2, box(width = NULL, title = strong("Grafico"), status = "primary",
shinycssloaders::withSpinner(image = "www/running_olive.gif", plotly::plotlyOutput("boxttest_conf"))))
)
) #end of fluidpage
), #end of tabpanel conf 2 gruppi
# Confronto tra più gruppi
tabPanel(
"Confronto tra più gruppi", value = "tabpananova_conf",
fluidPage(
fluidRow(
column(12, box(width = NULL, title = strong("Boxplot"), status = "primary",
shinycssloaders::withSpinner(image = "www/running_olive.gif", plotly::plotlyOutput("boxanova_conf"))))
),
fluidRow(
column(6, box(width = NULL, title = strong("Test sulla normalità"), status = "primary", verbatimTextOutput("shapiroanova1_conf"))),
conditionalPanel(
condition = "(output.shapanovamorfoui_conf == 'distribuzione normale' && (input.selectanovatest2_conf == 'ANOVA' || input.selectanovatest2_conf == 'Kruskal-Wallis')) || (output.shapanovamorfoui_conf == 'distribuzione non normale' && input.selectanovatest2_conf == 'Kruskal-Wallis')",
conditionalPanel(condition = "input.selectanovatest2_conf == 'ANOVA'",
column(6, box(width = NULL, title = strong("Test ANOVA"), status = "primary", verbatimTextOutput("anova1morfoprint_conf")))
),
conditionalPanel(condition = "input.selectanovatest2_conf == 'Kruskal-Wallis'",
column(6, box(width = NULL, title = strong("Test Kruskal-Wallis"), status = "primary", verbatimTextOutput("kruskmorfo_conf")))
)
),
conditionalPanel(condition = "output.shapanovamorfoui_conf == 'distribuzione non normale' && input.selectanovatest2_conf == 'ANOVA'",
column(6, box(width = NULL, title = strong("Test ANOVA"), status = "warning", style = "text-align: justify; text-align: center;",
tags$i(class = "fas fa-exclamation-triangle", style="font-size: 25px; color: rgb(243,156,18)"),
h4(strong("La variabile numerica non segue la distribuzione normale. Scegli il test Kruskal-Wallis.", style = "color: rgb(243,156,18)")),
))
)
),
conditionalPanel(
condition = "(output.shapanovamorfoui_conf == 'distribuzione normale' && (input.selectanovatest2_conf == 'ANOVA' || input.selectanovatest2_conf == 'Kruskal-Wallis')) || (output.shapanovamorfoui_conf == 'distribuzione non normale' && input.selectanovatest2_conf == 'Kruskal-Wallis')",
fluidRow(
column(10,offset = 1,
box(width = NULL, title = strong("Post-hoc"), status = "primary", style = "text-align: justify; text-align: center;",
conditionalPanel(
condition = "output.signiftestmorfoui_conf == 'significativo'",
conditionalPanel(condition = "input.selectanovatest2_conf == 'ANOVA'",
h4(strong("Tukey HSD"))),
conditionalPanel(condition = "input.selectanovatest2_conf == 'Kruskal-Wallis'",
h4(strong("Dunn Test")),
),
shinycssloaders::withSpinner(image = "www/running_olive.gif", plotly::plotlyOutput("posthocmorfograph_conf"))
),
conditionalPanel(condition = "output.signiftestmorfoui_conf == 'non significativo'",
tags$i(class = "fas fa-exclamation-triangle", style="font-size: 25px; color: rgb(243,156,18)"),
h4(strong("Il p-value è maggiore del livello di significatività impostato. Non ci sono differenze significative tra le variabili.", style = "color: rgb(243,156,18)"))
)
)
)
) #end of fluidrow post-hoc
)
) #end of fluidpage
), #end of tabpanel più gruppi
#
#
#
#
# #Test d'indipendenza
# tabPanel("Test d'indipendenza", value = "tabpanchisqtestmorfo",
# br(),
# fluidPage(
# fluidRow(
# column(5, box(width = NULL, title = strong("Tabella di contingenza"), status = "primary", tableOutput("contingtablemorfo"))),
# column(6,
# fluidRow(
# box(width = NULL, title = strong("Test"), status = "primary", verbatimTextOutput("chisqmorfoprint"))
# ),
#
# fluidRow(
# conditionalPanel(condition = "output.signiftestchisqmorfoui == 'significativo'",
# #box(width = NULL, title = strong("Grafico residui"), status = "primary", style = "text-align: justify; text-align: center;",
# shinycssloaders::withSpinner(image = "www/running_olive.gif", plotOutput("plotresidchisq"))
# # )
#
# ),
# conditionalPanel(condition = "output.signiftestchisqmorfoui == 'non significativo'",
# box(width = NULL, status = "warning", style = "text-align: justify; text-align: center;",
# tags$i(class = "fas fa-exclamation-triangle", style="font-size: 25px; color: rgb(243,156,18)"),
# h4(strong("Il p-value è maggiore del livello di significatività impostato. Le variabili sono indipendenti.", style = "color: rgb(243,156,18)"))
# )
# )
# ) #end of fluidrow grafico
# )
# ) #end of first fluidrow
# )
# )
) #end of tabset panel
),
)# end tabbox integrazione
)
)
) #end tabitem integrazione
)#end of tabitems
)#end of dashboardbody
)#end of dashboardpage
)
)
) #end of taglist
}
#' Add external Resources to the Application
#'
#' This function is internally used to add external
#' resources inside the Shiny application.
#'
#' @import shiny
#' @importFrom golem add_resource_path activate_js favicon bundle_resources
#' @noRd
golem_add_external_resources <- function(){
add_resource_path(
'www', app_sys('app/www')
)
tags$head(
favicon(),
bundle_resources(
path = app_sys('app/www'),
app_title = 'OliveHealthR'
)
# Add here other external resources
# for example, you can add shinyalert::useShinyalert()
)
}
ShinyFabio/OliveHealthR2 documentation built on Oct. 18, 2024, 2:22 a.m.
R Package Documentation
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Defines functions golem_add_external_resources app_ui
#' The application User-Interface
#'
#' @param request Internal parameter for `{shiny}`.
#' DO NOT REMOVE.
#' @import shiny
#' @import shinydashboard
#' @import shinyWidgets
#' @importFrom plotly plotlyOutput
#' @import tmap
#' @import tmaptools
#' @import htmltools
#' @importFrom DT DTOutput
#' @importFrom shinycssloaders withSpinner
#' @importFrom shinyjs hidden
#' @importFrom InteractiveComplexHeatmap InteractiveComplexHeatmapOutput
#' @noRd
app_ui <- function(request) {
tagList(
tags$head(tags$style(type = 'text/css', ".navbar-default{display:none;}")), #rimuove la barra "Home | Codice"
# Leave this function for adding external resources
golem_add_external_resources(),
shinyjs::useShinyjs(),
# Your application UI logic
navbarPage(title = "OliveHealthR", theme = "www/spacelab.min.css",
id = "navb1",
#margin-right:auto; margin-left:auto;
tags$head(tags$style(type = "text/css", ".container-fluid{padding-left:0px; padding-right:0px ; }")),
tabPanel(title = "Welcome", value = "panel1",
tags$img(src = "www/Photo_2.jpg", width = "100%"),
h2(strong("Cos'è OliveHealthR?"), style = "text-align: center"),
br(), br(),
fluidRow(
column(1, offset=1,tags$img(src = "www/OliveHealthRfavicon.png", width = "173", height = "200")),
column(width = 6, offset = 1,
p(h4("OliveHealthR è un software che svolge analisi sui dati provenienti dal progetto OliveHealth. L'obiettivo principale del progetto è quello di identificare le
componenti salutistiche (es. polifenoli) in prodotti della filiera olivicola (quali foglie, drupe e
olio) correlandole alla geo-localizzazione di ciascun appezzamento. Sulla base di queste informazioni
verranno prodotti dataset delle variabili rappresentative delle principali caratteristiche fenotipiche,
biochimiche e genetiche associate all’ulivo dalle quali nascerà un database messo a disposizione ai
produttori olivicoli campani.", "Per maggiori informazioni sul progetto clicca",
strong(a(href = "https://olivehealth.it", "qui", .noWS = "after"), .noWS = "after"),
".", style = "font-family:'Quicksand', Sans-serif; font-weight: 400; line-height: 1.5; text-align: justify;"
)),
),
column(1, offset = 1, tags$img(src = "www/Olivehealt_Logo.png", width = "200", height = "200"))
),
fluidRow(column(1, offset = 5,
br(),
actionButton("jumpToP2", label = HTML(" VAI!"), icon("rocket"), class = "btn btn-primary btn-lg", width = "200px", style='padding:10px; font-size:200%; font-weight: bold;')
)
),
p(h4("Questo progetto è stato finanziato da:")),
fluidRow(
column(1, tags$img(src = "www/Logo_AprolCampania.jpg", width = "225", height = "150")),
column(2, offset = 4, tags$img(src = "www/CNR.png", width = "150", height = "155")),
column(3, offset = 2, tags$img(src = "www/stringa-2.png", width = "423", height = "110"))
)
),
##### Lista menuItem ####
tabPanel(title = "Codice", value = "panel2",
shinyBS::bsModal("keybutton_modal", "Inserisci codice", trigger = "keybutton", size = "small",
br(),textInput("ins_passw", label = "", placeholder = "Scrivi qui il codice.")),
dashboardPage(
dashboardHeader(title = "OliveHealthR",
tags$li(class = "dropdown",
actionBttn("keybutton", icon = icon("key"), style = "stretch", size = "lg" , color = "primary"),
actionBttn("jumptohome", icon = icon("home"), style = "stretch", size = "lg" , color = "primary")
)),
dashboardSidebar(
sidebarMenu(
menuItem("File", tabName = "filemenuitem", icon = icon("file-import")),
menuItem("Azienda", tabName = "azienda", icon = icon("id-card")),
menuItem("Campionamento azienda", tabName = "campazienda", icon = icon("file-alt"),
menuSubItem("Drupe e foglie", tabName = "drupleafsub"),
menuSubItem("Olio", tabName = "oliosub"),
menuSubItem("Calendario campionamenti", tabName = "calendar"),
shinyjs::hidden(menuSubItem("Analisi sensoriali", tabName = "assaggsub"))),
menuItem("Analisi laboratorio", tabName = "anlab", icon = icon("flask"),
menuSubItem("Polifenoli totali", tabName = "totpolsub"),
menuSubItem("Polifenoli individuali", tabName = "inpolsub"),
shinyjs::hidden(menuSubItem("Polifenoli LCxLC", tabName = "lcpolsub")),
menuSubItem("Analisi morfometrica", tabName = "anmorfosub")),
menuItem("Integrazione dati", tabName = "integrdati", icon = icon("vials"))
)
),
dashboardBody(
tabItems(
##### tabitem File ####
tabItem(tabName = "filemenuitem",
fluidRow(
#schede aziende
column(3,
box(width = NULL, status = "primary", title = h3(strong("Aziende"), style = "color: white; display:inline; margin-top: 0px;margin-bottom: 0px;"), solidHeader = T,
uiOutput("valbox_aziende")
)
),
#schede campionamento
column(3,
box(width = NULL, status = "primary", title = h3(strong("Schede campionamento"), style = "color: white; display:inline; margin-top: 0px;margin-bottom: 0px;"), solidHeader = T,
uiOutput("valbox_drupecamp"),
uiOutput("valbox_oliocamp"),
uiOutput("valbox_assaggi")
)
),
#polifenoli
column(3,
box(width = NULL, status = "primary", title = h3(strong("Polifenoli"), style = "color: white; display:inline; margin-top: 0px;margin-bottom: 0px;"), solidHeader = T,
uiOutput("valbox_poltot"),
uiOutput("valbox_polind")
)
),
#morfometria
column(3,
box(width = NULL, status = "primary", title = h3(strong("Morfometria"), style = "color: white; display:inline; margin-top: 0px;margin-bottom: 0px;"), solidHeader = T,
uiOutput("valbox_morfo"))
)
), #end of fluidrow
fluidRow(
column(4, offset = 4, style = "text-align:center;", br(), br(), br(), br(), br(),
actionButton("load_files", label = HTML(" Carica tutti dati!"), icon("file-upload"), class = "btn btn-primary btn-lg", width = "300px", style='padding:10px; font-size:200%; font-weight: bold;')
)
)
),
##### tabItem Azienda ####
tabItem(tabName = "azienda",
tabBox(width = 12,
tabPanel(tagList(shiny::icon("table"), HTML(" Tabella")),
box(width = NULL, status = "primary", style = "overflow-x: scroll;",
DT::DTOutput("content")
)
#mod_update_data_ui("updataaziende")
),
tabPanel(tagList(shiny::icon("chart-bar"), HTML(" Cultivar")),
box(width=NULL, status = "primary", h4(htmlOutput("numcult"))),
br(),
fluidRow(
column(2,
box(width = NULL, status = "primary",
radioButtons("selplotcult", label = h4("Tipo di grafico"), choices = list("Grafico a torta" = 1, "Grafico a barre" = 2), selected = 2))
),
column(width=10, box(width=NULL, status = "primary", shinycssloaders::withSpinner(image = "www/running_olive.gif", uiOutput("cultplot"))))
)
),
#### dati meteo
tabPanel(
tagList(shiny::icon("cloud-sun-rain"), HTML(" Dati meteo")),
sidebarLayout(
sidebarPanel(
width = 2,
selectInput("varmeteo",
label = tags$span("Variabile meteo", circleButton("hintmeteo", icon = icon("info"), status = "info", size = "xs")),
choices = c("Precipitazioni totali" = "tp",
"Volume d'acqua nel suolo (7-28cm)" = "swvl2",
"Volume d'acqua nel suolo (28-100cm)" = "swvl3")
),
shinyBS::bsPopover(
id = "hintmeteo",
title = "Variabili meteo",
content = paste0(
"Per ulteriori informazioni sulle misure di precipitazione clicca sul seguente link ",
a("copernicus.eu", href = "https://cds.climate.copernicus.eu/cdsapp#!/dataset/reanalysis-era5-land-monthly-means?tab=overview", target="_blank")
),
placement = "right",
trigger = c("hover","click"),
options = list(container = "body")
),
conditionalPanel(
condition = "input.tabsetmeteo == 'tabpanmeteomap'",
awesomeRadio("type_mapmeteo", "Tipo di mappa", choices = c("Statica","Animata")),
selectInput("selyearmeteo", "Seleziona anno", choices = "")
),
conditionalPanel(
condition = "input.tabsetmeteo == 'tabpanplotomap'",
awesomeRadio("meteoplot_tipoconf", "Tipo di confronto", choices = c("Tra anni", "Tra aziende"))
)
),
mainPanel(
width = 10,
tabsetPanel(id = "tabsetmeteo",
tabPanel("Mappa", value = "tabpanmeteomap",
conditionalPanel(condition = "input.type_mapmeteo == 'Animata'",
fluidPage(
shinycssloaders::withSpinner(imageOutput("mapmeteo"), image = "www/running_olive.gif"))
),
conditionalPanel(
condition = "input.type_mapmeteo == 'Statica'",
shinycssloaders::withSpinner(tmapOutput("mapmeteo2"))
)
),
tabPanel("Plot", value = "tabpanplotomap",
box(width=NULL, status = "primary",
fluidRow(
conditionalPanel(
condition = "input.meteoplot_tipoconf == 'Tra aziende'",
column(2, awesomeRadio("type_lineplot", "Tipo di grafico", choices = c("Statico","Animato"))),
column(3, selectInput("selyearplotmeteo", "Seleziona anno", choices = "Tutti")),
column(3, selectInput("selcod_plotmeteo", "Scegli una o più aziende", choices = "", multiple = TRUE))
),
conditionalPanel(
condition = "input.meteoplot_tipoconf == 'Tra anni'",
column(3, selectInput("selcod_plotmeteo2", "Scegli un'azienda", choices = ""))
)
)),
conditionalPanel(
condition = "input.type_lineplot == 'Statico'",
shinycssloaders::withSpinner(plotly::plotlyOutput("ggline_meteo"), image = "www/running_olive.gif")
),
conditionalPanel(
condition = "input.type_lineplot == 'Animato' && input.meteoplot_tipoconf == 'Tra aziende'",
shinycssloaders::withSpinner(imageOutput("plotline_animated"), image = "www/running_olive.gif")
)
)
)
)
)
), #end of tabbox dati meteo
# Mappa azienda
tabPanel(tagList(shiny::icon("map-marked-alt"), HTML(" Mappa")),
sidebarLayout(
sidebarPanel(width = 3,
div(actionButton("update", "Carica mappa", class = "btn-primary", style = 'padding:4px; font-size:160%'), align = "center"),
hr(),
selectInput("select3", "Seleziona la colonna da visualizzare", choices = "", multiple = FALSE),
selectInput("filt_cult_mapp", "Filtra per cultivar", choices = "", multiple = TRUE)
),
mainPanel(width = 9,
conditionalPanel(condition = "input.update != 0",
shinycssloaders::withSpinner(tmapOutput("map1",height = 650)),
)
)
)
)
) #end of tabset
),
##### TabItem Campionamento Azienda ####
##### campionamento foglie e drupe #########################################
tabItem(tabName = "drupleafsub",
tabBox(width = 12,
tabPanel(
tagList(shiny::icon("table"), HTML(" Tabella")),
#qui aggiungere la tabella drupe foglie
fluidPage(
box(width = NULL, status = "primary", style = "overflow-x: scroll;",
DT::DTOutput("tabledrupscheda")),
#mod_update_data_ui("updatadrupe")
)
),
tabPanel(tagList(shiny::icon("chart-bar"), HTML(" Grafici")),
#qui i grafici drupe foglie
sidebarLayout(
sidebarPanel(width = 2,
selectInput("selectx", "Seleziona la colonna X", choices = "", multiple = FALSE),
selectInput("selecty", "Seleziona la colonna Y", choices = "", multiple = FALSE)
),
mainPanel(width = 10,
tabsetPanel(
tabPanel("Scatter plot",
br(),
box(width=NULL, status = "primary",
fluidRow(
column(3, selectInput("selyearscatter", "Seleziona l'anno", choices = "", multiple = FALSE)),
column(3, selectInput("num2", "Scegli il numero di campionamento", choices = c("1" = "R1", "2" = "R2"), selected = "R1", multiple = FALSE)),
column(3, selectInput("selectfill", "Colonna da usare come riempimento", choices = "", multiple = FALSE))
)),
shinycssloaders::withSpinner(plotly::plotlyOutput("plotxy"), image = "www/running_olive.gif")
),
tabPanel("Barplot",
fluidRow(column(width = 2, br(),
box(width = NULL, status = "primary", checkboxGroupInput("checkcamp", "Seleziona campionamento", choices = ""))
),
column(width = 10, br(),
box(width=NULL, status = "primary",
shinycssloaders::withSpinner(plotly::plotlyOutput("barplot1"), image = "www/running_olive.gif"))
)
)
)#end of tabpanel
)#end of tabset
)#end of mainpanel
)#end of sidebarlayout
), #end of tabpanel grafici
tabPanel(tagList(shiny::icon("images"), HTML(" Galleria")),
#qui le foto drupe foglie
fluidPage(
fluidRow(
column(width=4,
fluidRow(
column(6,
box(width = NULL, status = "primary",
radioGroupButtons(inputId = "campfoto", label = "Numero campionamento", choices = c("1" = "1_campionamento", "2" = "2_campionamento"),
individual = TRUE, checkIcon = list(yes = tags$i(class = "fa fa-circle", style = "color: steelblue"), no = tags$i(class = "fa fa-circle-o", style = "color: steelblue")))
)
),
column(6, box(width=NULL, status = "primary",
selectInput("selyearfoto", "Seleziona l'anno", choices = "", multiple = FALSE)
))
),
fluidRow(column(12, box(width=NULL, status = "primary", style = "overflow-x: scroll;", DT::DTOutput("prov2"))))
),
conditionalPanel(condition = "input.prov2_rows_selected == 0",
p(strong(h4("Per favore seleziona un'azienda dalla tabella", align = "center")))
),
conditionalPanel(condition = "input.prov2_rows_selected != 0",
column(width = 4, box(width=NULL, status = "primary", title = "Foglie", align= "center", uiOutput("phfoglia"))),
column(width = 4, box(width=NULL, status = "primary", title = "Drupe",align = "center", uiOutput("phdrupa")))
)
) #end of fluidRow
)
), #end of tabpanel foto
tabPanel(tagList(shiny::icon("map-marked-alt"), HTML(" Mappa")),
mod_render_map_ui("modulo_mappa_datadrupe")
) #end of tabpanel mappa drupe foglie
) #end of tabBox
), #end of tabitem drupe foglie
##### campionamento olio #########################################
tabItem(tabName = "oliosub",
tabBox(width = 12,
tabPanel(tagList(shiny::icon("table"), HTML(" Tabella")),
#qui aggiungere la tabella drupe foglie
fluidPage(
box(width = NULL, status = "primary", style = "overflow-x: scroll;",
DT::DTOutput("tableolioscheda")),
)
),
tabPanel(tagList(shiny::icon("map-marked-alt"), HTML(" Mappa")),
sidebarLayout(
sidebarPanel(
width = 3,
div(actionButton("updateoilmap", "Carica mappa", class = "btn-primary", style = 'padding:4px; font-size:160%'), align = "center"),
conditionalPanel(condition = "input.updateoilmap != 0",
hr(),
selectInput("selcoloilmap", "Seleziona la colonna da visualizzare", choices = "", multiple = FALSE),
selectInput("selyearoilmap", "Seleziona l'anno", choices = "", multiple = FALSE)
)
),
mainPanel(width = 9,
conditionalPanel(condition = "input.updateoilmap != 0",
shinycssloaders::withSpinner(tmapOutput("mapolio"))),
)
)
)
)
),
##### Calendario #########
tabItem(tabName = "calendar",
sidebarLayout(
sidebarPanel(width = 2,
awesomeRadio("selfilecalend", "Seleziona il tipo di campionamento", choices = ""),
conditionalPanel(condition = "input.selfilecalend == 'Drupe e foglie'",
awesomeRadio("selcampcalend", "Seleziona il numero di campionamento", choices = c("Entrambi", "R1", "R2")),
),
selectInput("selyearcalend", "Seleziona l'anno", choices = "", multiple = FALSE),
selectInput("selaziendacalend", "Scegli l'azienda", choices = "", multiple = FALSE),
),
mainPanel(width = 10,
shinycssloaders::withSpinner(image = "www/running_olive.gif",plotOutput("yearcalendar", height = "700px"))
)
)
),
###### Assaggi sensoriali ########
tabItem(tabName = "assaggsub",
tabBox(width = 12,
#tabella
tabPanel(tagList(shiny::icon("table"), HTML(" Tabella")),
box(width = NULL, status = "primary", style = "overflow-x: scroll;",
DT::DTOutput("tableassaggischeda")),
),
#grafici
tabPanel(
tagList(shiny::icon("chart-bar"), HTML(" Grafici")),
tabsetPanel(
tabPanel("Scatter plot",
sidebarLayout(
sidebarPanel(width = 2,
selectInput("selectxassaggiscatt", "Seleziona la colonna X", choices = "", multiple = FALSE),
selectInput("selectyassaggiscatt", "Seleziona la colonna Y", choices = "", multiple = FALSE),
),
mainPanel(width = 10,
br(),
box(width=NULL, status = "primary",
fluidPage(
fluidRow(
column(3, selectInput("selyearscatterassagg", "Seleziona l'anno", choices = "", multiple = FALSE)),
column(3, selectInput("selectfillassaggi", "Colonna da usare come riempimento", choices = "", multiple = FALSE))
))),
shinycssloaders::withSpinner(image = "www/running_olive.gif", plotly::plotlyOutput("scattplotassagg"))
)
)
), #end of tabpanel scatter plot
tabPanel("Barplot",
sidebarLayout(
sidebarPanel(width = 2,
awesomeRadio("barplotassaggi", "Tipo di barplot", choices = c("Affiancato" = "dodge", "Impilato" = "stack")),
selectInput("selyearbarassagg", "Seleziona l'anno", choices = "", multiple = FALSE),
),
mainPanel(width = 10,
br(),
shinycssloaders::withSpinner(image = "www/running_olive.gif", plotly::plotlyOutput("barplotassagg"))
)
)
), #end of tabpanel barplot
tabPanel("Spiderplot",
sidebarLayout(
sidebarPanel(width = 2,
selectInput("selyearspiderassaggi", "Seleziona l'anno", choices = "", multiple = FALSE),
selectInput("selcodspiderassaggi1", "Seleziona un'azienda", choices = "", multiple = FALSE),
awesomeCheckbox("addcodspiderassaggi", "Aggiungi seconda azienda", value = FALSE),
conditionalPanel(condition = "input.addcodspiderassaggi == true",
selectInput("selcodspiderassaggi2", "Seleziona un'azienda", choices = "", multiple = FALSE)
)
),
mainPanel(width = 10,
div(shinycssloaders::withSpinner(image = "www/running_olive.gif", plotOutput("assaggispider", width = "100%",height = "600px")), align = "center"),
)
)
) #end of tabpanel spiderplot
) #end of tabsetpanel
), #end of tabpanel grafici
#galleria
tabPanel(tagList(shiny::icon("images"), HTML(" Galleria")),
fluidPage(
fluidRow(
column(width=4,
fluidRow(
column(6, box(width=NULL, status = "primary",
selectInput("selyearallegatph", "Seleziona l'anno", choices = "", multiple = FALSE))
)
),
fluidRow(column(12, box(width=NULL, status = "primary", DT::DTOutput("dtallegato"))))
),
column(width = 8,
column(width = 6, offset = 3,
conditionalPanel(condition = "input.dtallegato_rows_selected == 0",
box(width = NULL, background = "yellow", tags$i(class = "fas fa-exclamation-triangle", style="font-size: 27px"), h4(strong("Seleziona un'azienda dalla tabella"), style = "color: white"), style = "text-align: justify; text-align: center;"),
)
),
conditionalPanel(condition = "input.dtallegato_rows_selected != 0",
uiOutput("phallegati")
)
)
) #end of fluidRow
)
),
#mappa
tabPanel(tagList(shiny::icon("map-marked-alt"), HTML(" Mappa")),
mod_render_map_ui("modulo_mappa_assaggi")
) #end of tabpanel mappa assaggi
) #end of tabBox
), #end of tabItem
##### TabItem Analisi Laboratorio #####
# Tab polifenoli totali ----------------------------------------------------------------
tabItem(tabName = "totpolsub",
sidebarLayout(
sidebarPanel(width = 2,
radioGroupButtons("selfilepoltot", "Seleziona i polifenoli da analizzare",
choiceValues = list("foglie", "drupe", "olio", "posa", "sansa"),
choiceNames = list(
paste(shiny::icon("leaf", style='font-size:16px;'), HTML("<b style=font-size:16px> Foglie</b>")),
paste(tags$img(src = "www/olive_icon2.png", height = "22px", width = "22px"), HTML("<b style=font-size:16px> Drupe</b>")),
paste(tags$img(src = "www/olive_oil.png", height = "22px", width = "22px"), HTML("<b style=font-size:16px> Olio</b>")),
paste(tags$img(src = "www/posa.png", height = "22px", width = "22px"), HTML("<b style=font-size:16px> Posa</b>")),
paste(tags$img(src = "www/sansa3.png", height = "23px", width = "23px"), HTML("<b style=font-size:16px> Sansa</b>"))),
direction = "vertical", justified = TRUE, status = "primary"
),
hr(),
conditionalPanel(condition = "input.tabboxpoltot == 'tabdtpoltot' || (input.tabboxpoltot == 'tabpoltotgraph' && input.boxpoltotgraph == 'boxscattpoltot')",
materialSwitch(inputId = "summpoltot", label = "Sintetizza i dati", value = TRUE, status = "primary")
),
conditionalPanel(
condition = "input.tabboxpoltot == 'tabpoltotgraph'",
h4(strong("Impostazioni grafici")),
#scatterplot
conditionalPanel(condition = "input.boxpoltotgraph == 'boxscattpoltot'",
selectInput("selectxtot", "Seleziona la colonna X", choices = "", multiple = FALSE),
selectInput("selectytot", "Seleziona la colonna Y", choices = "", multiple = FALSE)
),
#barplot
conditionalPanel(condition = "input.boxpoltotgraph == 'boxbarpoltot'",
selectInput("selectytotbar", "Seleziona la colonna Y", choices = "", multiple = FALSE),
selectInput("selectfilltotbar", "Colonna da usare come riempimento", choices = c("N_campionamento", "Cultivar_principale"), selected = "N_campionamento"),
hr(),
checkboxGroupInput("checkcamptot", "Seleziona campionamento", choices = "")
)
),
# MAPPA __________________________________________________________
conditionalPanel(condition = "input.tabboxpoltot == 'tabpoltotmap'",
div(actionButton("updatepoltotmap", "Carica mappa", class = "btn-primary", style = 'padding:4px; font-size:160%'), align = "center"),
conditionalPanel(condition = "input.updatepoltotmap != 0",
hr(),
selectInput("colpoltotmap1", "Seleziona la colonna da visualizzare", choices = "", multiple = FALSE),
selectInput("yearpoltotmap1", "Seleziona l'anno", choices = "", multiple = FALSE),
selectInput("numpoltotmap1", "Scegli il numero di campionamento", choices = "", multiple = FALSE),
hr(),
div(actionButton("addmappoltot2", label = "Aggiungi seconda mappa"), align = "center"),
),
conditionalPanel(condition = "input.addmappoltot2 != 0",
br(),
selectInput("colpoltotmap2", "Seleziona la colonna da visualizzare", choices = "", multiple = FALSE),
selectInput("yearpoltotmap2", "Seleziona l'anno", choices = "", multiple = FALSE),
selectInput("numpoltotmap2", "Scegli il numero di campionamento", choices = "", multiple = FALSE),
)
)
),
mainPanel(width = 10,
tabBox(id = "tabboxpoltot", width = NULL,
tabPanel(tagList(shiny::icon("table"), HTML(" Tabella")), value = "tabdtpoltot",
fluidPage(
box(width = NULL, status = "primary", style = "overflow-x: scroll;",
DT::DTOutput("tablepoltot")),
#mod_update_data_ui("updatapol"),
br(),
mod_render_NAbox_ui("naboxpoltot")
)
), #end of tabpanel tabella
tabPanel(tagList(shiny::icon("chart-bar"), HTML(" Grafici")), value = "tabpoltotgraph",
tabsetPanel(id = "boxpoltotgraph",
tabPanel("Scatter plot", value = "boxscattpoltot",
box(width=NULL, status = "primary",
fluidRow(
column(3, selectInput("selyearscattertot", "Seleziona l'anno", choices = "", multiple = FALSE)),
column(3, selectInput("numtot", "Scegli il numero di campionamento", choices = "", multiple = FALSE)),
column(3, selectInput("selectfilltot", "Colonna da usare come riempimento", choices = "", multiple = FALSE))
)),
shinycssloaders::withSpinner(image = "www/running_olive.gif", plotly::plotlyOutput("totscatplot"))
), #end of tabpanel scatter plot
tabPanel("Barplot", value = "boxbarpoltot",
shinycssloaders::withSpinner(image = "www/running_olive.gif", plotly::plotlyOutput("barplottot"))
) #end of tabpanel barplot
) #end of tabsetpanel grafici
), #end of tabpanel grafici
#tabpanel mappa
tabPanel(tagList(shiny::icon("map-marked-alt"), HTML(" Mappa")), value = "tabpoltotmap",
conditionalPanel(condition = "input.updatepoltotmap != 0",
shinycssloaders::withSpinner(tmapOutput("poltotmap1"))),
conditionalPanel(condition = "input.addmappoltot2 != 0",
hr(),
shinycssloaders::withSpinner(tmapOutput("poltotmap2")))
)
) #end of tabbox poltot
) #end of mainpanel
)#end of sidebarlayout
), #end of tabitem "totpolsub"
# Tab polifenoli individuali ----------------------------------------------------------------------------
tabItem(tabName = "inpolsub",
sidebarLayout(
sidebarPanel(width = 2,
radioGroupButtons("selfilepolind", "Seleziona i polifenoli da analizzare",
choiceValues = list("foglie", "drupe", "olio", "posa"),
choiceNames = list(
paste(icon("leaf", style='font-size:16px;'), HTML("<b style=font-size:16px> Foglie</b>")),
paste(tags$img(src = "www/olive_icon2.png", height = "22px", width = "22px"), HTML("<b style=font-size:16px> Drupe</b>")),
paste(tags$img(src = "www/olive_oil.png", height = "22px", width = "22px"), HTML("<b style=font-size:16px> Olio</b>")),
paste(tags$img(src = "www/posa.png", height = "22px", width = "22px"), HTML("<b style=font-size:16px> Posa</b>"))
),
direction = "vertical", justified = TRUE, status = "primary"
),
hr(),
conditionalPanel(
condition = "input.tabboxpolind == 'tabdtpolind' || input.tabboxpolind == 'tabpolindpca' ||
(input.tabboxpolind == 'tabpolindgraph' && input.boxpolindgraph == 'boxscattpolind' )",
materialSwitch(inputId = "summpolind", label = "Sintetizza i dati", value = TRUE, status = "primary")
),
conditionalPanel(
condition = "input.tabboxpolind == 'tabpolindgraph'",
h4(strong("Impostazioni grafici")),
# Scatterplot ______________________________________________________
conditionalPanel(condition = "input.boxpolindgraph == 'boxscattpolind'",
selectInput("selectxind", "Seleziona la colonna X", choices = "", multiple = FALSE),
selectInput("selectyind", "Seleziona la colonna Y", choices = "", multiple = FALSE)
),
# Boxplot ______________________________________________________
conditionalPanel(condition = "input.boxpolindgraph == 'boxboxplotpolind'",
selectInput("selectyboxind", "Seleziona un polifenolo", choices = "", multiple = FALSE)
),
# Barplot ____________________________________________________________
conditionalPanel(condition = "input.boxpolindgraph == 'boxbarpolind'",
selectInput("selectyindbar", "Seleziona un polifenolo", choices = "", multiple = FALSE),
selectInput("selectfillindbar", "Colonna da usare come riempimento", choices = c("N_campionamento", "Cultivar_principale"), selected = "N_campionamento"),
hr(),
checkboxGroupInput("checkcampind", "Seleziona campionamento", choices = "")
),
# Heatmap _______________________________________________________
conditionalPanel(condition = "input.boxpolindgraph == 'boxheatpolind'",
div(actionButton("updateheat", label = "Carica!", class = "btn btn-primary btn-lg", width = "140px", style='padding:5px; font-size:150%; font-weight: bold;'), align= "center"),
br(),
h4(strong("Dati")),
selectInput("numheat", "Scegli il numero di campionamento", choices = "", multiple = FALSE),
selectInput("selyearheatind", "Seleziona l'anno", choices = "", multiple = FALSE),
hr(),
h4(strong("Preprocessing")),
selectInput("selscaleheat", "Scala i dati:", choices = c("No" = "none", "Per riga" = "row", "Per colonna" = "column"), selected = "none"),
hr(),
h4(strong("Opzioni dendrogramma")),
###voglio il dendrograma su riga o colonna o entrambi?
h5(strong("Scegli dove mostrare il dendrogramma")),
fluidRow(
column(6, materialSwitch(inputId = "rowdend", label = "Riga", value = TRUE, status = "primary", width = "90%")),
column(6, materialSwitch(inputId = "columndend", label = "Colonna", value = TRUE, status = "primary", width = "90%"))
),
selectInput("selectannot", "Colonna annotazione:", choices = c("Provincia", "Cultivar_principale", "Areale")),
conditionalPanel(condition = "input.rowdend == 1 || input.columndend == 1",
selectInput("seldistheatpol", "Funzione di distanza:", choices = c("euclidean", "maximum", "manhattan", "canberra", "minkowski"), selected = "euclidean"),
selectInput("selhclustheatpol", "Metodo clustering:", choices = c("ward.D", "ward.D2", "single", "complete", "average" , "mcquitty", "median", "centroid"), selected = "complete"),
),
conditionalPanel(condition = "input.rowdend == 0",
h5(strong("Ordinare i dati per annotazione?")),
awesomeCheckbox("heatsort", label = "Ordina", value = TRUE)
),
conditionalPanel(condition = "input.rowdend == 1",
hr(),
h4(strong("Dendrogramma su riga")),
sliderInput("sliderrowheat", "Numero cluster:", min = 2, max = 10, value = 2),
),
conditionalPanel(condition = "input.columndend == 1",
hr(),
h4(strong("Dendrogramma su colonna")),
uiOutput("sliderheatcol"),
)
), #end of conditional heatmap
# Spiderplot __________________________________________
conditionalPanel(condition = "input.boxpolindgraph == 'boxspiderpolind'",
awesomeRadio("type_spidind", "Tipo di confronto", choices = c("Tra aziende","Tra anni")),
#confronto tra aziende
conditionalPanel(condition = "input.type_spidind == 'Tra aziende'",
selectInput("selyearspiderpolind", "Seleziona l'anno", choices = "", multiple = FALSE),
selectInput("selcampspiderpolind", "Seleziona il numero di campionamento", choices = "", multiple = FALSE),
selectInput("selcodspiderpolind", "Seleziona un'azienda", choices = "", multiple = FALSE),
awesomeCheckbox("addcodspiderpolind", "Aggiungi seconda azienda", value = FALSE),
conditionalPanel(condition = "input.addcodspiderpolind == true",
selectInput("selcodspiderpolind2", "Seleziona un'azienda", choices = "", multiple = FALSE)
)
),
#confronto tra anni
conditionalPanel(
condition = "input.type_spidind == 'Tra anni'",
selectInput("selcodspidind", "Seleziona un'azienda", choices = "", multiple = FALSE),
selectInput("selcampspidind", "Seleziona il numero di campionamento", choices = "", multiple = FALSE)
)
),
# Correlation _________________________________________________________________
conditionalPanel(
condition = "input.boxpolindgraph == 'boxcorrpolind'",
selectInput("selyearcorrind", "Seleziona l'anno", choices = "", multiple = FALSE),
selectInput("numcorr", "Scegli il numero di campionamento", choices = "", multiple = FALSE)
),
), #end of conditional panel dei grafici
# PCA ____________________________________________________________________
conditionalPanel(
condition = "input.tabboxpolind == 'tabpolindpca'",
selectInput("selyearpca", "Seleziona l'anno", choices = "", multiple = FALSE),
selectInput("numpca", "Scegli il numero di campionamento", choices = "", multiple = FALSE),
radioGroupButtons(inputId = "selcorpca", label = "Matrice:", choices = c("Correlazione" = TRUE, "Covarianza" = FALSE),
individual = TRUE, checkIcon = list(yes = tags$i(class = "fa fa-circle", style = "color: steelblue"),no = tags$i(class = "fa fa-circle-o", style = "color: steelblue")))
),
# CLUSTERING _____________
conditionalPanel(
condition = "input.tabboxpolind == 'tabclustpolind'",
selectInput("selcolclustpolind", "Seleziona variabile", choices = c("Codice_azienda", "Cultivar_principale")),
selectInput("selyearclustpolind", "Seleziona l'anno", choices = "", multiple = TRUE),
selectInput("numclustpolind", "Scegli il numero di campionamento", choices = "", multiple = FALSE),
#materialSwitch(inputId = "summarizeclustmorfo", label = "Sintetizza i dati", status = "primary", value = TRUE),
radioGroupButtons("selclustmethodpolind", "Tipo di clustering", choices = c("Gerarchico", "Partizionale"), justified = TRUE, status = "primary"),
conditionalPanel(
condition = "input.selclustmethodpolind == 'Partizionale'",
selectInput("selclusthpolind", "Seleziona l'algoritmo di clustering", choices = c("K-means", "PAM", "Clara"), selected = "K-means", multiple = FALSE),
)
),
# MAPPA __________________________________________________________
conditionalPanel(condition = "input.tabboxpolind == 'tabpolindmap'",
div(actionButton("updatepolindmap", "Carica mappa", class = "btn-primary", style = 'padding:4px; font-size:160%'), align = "center"),
conditionalPanel(condition = "input.updatepolindmap != 0",
hr(),
selectInput("colpolindmap1", "Seleziona la colonna da visualizzare", choices = "", multiple = FALSE),
selectInput("yearpolindmap1", "Seleziona l'anno", choices = "", multiple = FALSE),
selectInput("numpolindmap1", "Scegli il numero di campionamento", choices = "", multiple = FALSE),
hr(),
div(actionButton("addmappolind2", label = "Aggiungi seconda mappa"), align = "center"),
),
conditionalPanel(condition = "input.addmappolind2 != 0",
br(),
selectInput("colpolindmap2", "Seleziona la colonna da visualizzare", choices = "", multiple = FALSE),
selectInput("yearpolindmap2", "Seleziona l'anno", choices = "", multiple = FALSE),
selectInput("numpolindmap2", "Scegli il numero di campionamento", choices = "", multiple = FALSE),
)
)
), #end of sidebarpanel
mainPanel(width = 10,
tabBox(id = "tabboxpolind", width = NULL,
tabPanel(tagList(shiny::icon("table"), HTML(" Tabella")), value = "tabdtpolind",
fluidPage(
box(width = NULL, status = "primary", style = "overflow-x: scroll;",
DT::DTOutput("tablepolind")),
mod_render_NAbox_ui("naboxpolind")
)
), #end of tabpanel tabella
tabPanel(tagList(shiny::icon("chart-bar"), HTML(" Grafici")), value = "tabpolindgraph",
tabsetPanel(id = "boxpolindgraph",
tabPanel("Scatter plot", value = "boxscattpolind",
box(width=NULL, status = "primary",
fluidRow(
column(3, selectInput("selyearscatterind", "Seleziona l'anno", choices = "", multiple = FALSE)),
column(3, selectInput("numind", "Scegli il numero di campionamento", choices = "", multiple = FALSE)),
column(3, selectInput("selectfillind", "Colonna da usare come riempimento", choices = "", multiple = FALSE))
)),
shinycssloaders::withSpinner(image = "www/running_olive.gif", plotly::plotlyOutput("scatterindpol"))
), #end of tabpanel scatterplot
tabPanel("Boxplot", value = "boxboxplotpolind",
box(width=NULL, status = "primary",
fluidRow(
column(3, selectInput("selyearboxind", "Seleziona l'anno", choices = "", multiple = FALSE)),
column(3, selectInput("numboxind", "Scegli il numero di campionamento", choices = "", multiple = FALSE)),
column(3, selectInput("selectfillboxind", "Colonna da usare come riempimento", choices = "", multiple = FALSE))
)),
shinycssloaders::withSpinner(image = "www/running_olive.gif", plotly::plotlyOutput("boxplotindpol"))
),
tabPanel("Barplot", value = "boxbarpolind",
shinycssloaders::withSpinner(image = "www/running_olive.gif", plotly::plotlyOutput("barplotind"))
), #end of tabpanel barplot
tabPanel("Heatmap", value = "boxheatpolind",
InteractiveComplexHeatmap::InteractiveComplexHeatmapOutput("heatmap_polind_output", layout = "1|(2-3)", width1 = 850, height1 = 550)
),
tabPanel("Correlation Plot", value = "boxcorrpolind",
shinycssloaders::withSpinner(image = "www/running_olive.gif", plotly::plotlyOutput("corrplotind"))
), #end of tabpanel correlation
tabPanel(
"Spiderplot",
value = "boxspiderpolind",
div(shinycssloaders::withSpinner(image = "www/running_olive.gif", plotOutput("spider_polind", width = "100%",height = "600px")), align = "center"),
)
) #end of tabsetpanel
), #end of tabPanel Grafici
tabPanel(tagList(shiny::icon("chart-line"), HTML(" PCA")), value = "tabpolindpca",
tabsetPanel(
tabPanel("Plot",
br(),
fluidPage(
fluidRow(
column(3, box(width = NULL, status = "primary",
awesomeRadio("selbiplotpolind", "Seleziona tipo di grafico", choices = c("Biplot", "Plot")))),
column(4, box(width = NULL, status = "primary",
selectInput("colbiplot", "Seleziona colonna riempimento", choices = c("Codice_azienda", "Cultivar_principale", "Azienda", "Provincia", "Areale")))),
column(4, box(width = NULL, status = "primary",
awesomeCheckboxGroup("shpbiplot", "Aggiungi geometria", choices = "Provincia", inline = TRUE)
))),
shinycssloaders::withSpinner(image = "www/running_olive.gif", plotly::plotlyOutput("biplot", height = "500px")))
),
tabPanel("Screeplot",
br(),
shinycssloaders::withSpinner(image = "www/running_olive.gif", plotly::plotlyOutput("screeplot", width = "75%"))
),
tabPanel("Loadings",
fluidPage(
br(),
fluidRow(column(4, box(width = NULL, status = "primary", uiOutput("sliderpc")))),
shinycssloaders::withSpinner(image = "www/running_olive.gif", plotly::plotlyOutput("loadings"))
)
),
tabPanel("Plot 3D",
fluidPage(
br(),
fluidRow(
column(4, box(width = NULL, status = "primary",
selectInput("col3dind", "Seleziona colonna riempimento", choices = c("Codice_azienda", "Provincia", "Cultivar_principale", "Areale"))))
),
shinycssloaders::withSpinner(image = "www/running_olive.gif", plotly::plotlyOutput("pca3dpolind", height = "500px"))
)
)
) #end of tabsetpanel
), #end of tabpanel PCA
# Clustering
tabPanel(
tagList(tags$img(src = "www/clustering_icon.png", height = "16px", width = "16px"), HTML(" Clustering")), value = "tabclustpolind",
tabsetPanel(
tabPanel("Cluster plot",
br(),
fluidPage(
fluidRow(
column(
4,
box(width = NULL, status = "primary",
sliderInput("selnumclustpolind", "Numero cluster:", min = 1, max = 10, value = 2))),
column(
4,
conditionalPanel(
condition = "input.selclustmethodpolind == 'Gerarchico'",
box(width=NULL, status = "primary",
selectInput("selhclustmethpolind", "Seleziona metodo agglomerazione", choices = c("single", "complete", "ward.D", "ward.D2"), selected = "ward.D2"))
)
)
),
shinycssloaders::withSpinner(image = "www/running_olive.gif", plotOutput("plotclusterpolind", height = "600px"))
)
),
tabPanel("Numero cluster",
br(),
shinycssloaders::withSpinner(image = "www/running_olive.gif", plotOutput("numclustergraphpolind", height = "800px"))
)
)
), #end of tabpanel clustering
#tab galleria (ovvero i cromatogrammi)
tabPanel(tagList(shiny::icon("images"), HTML(" Galleria")), value = "tabpolindcroma",
fluidPage(
fluidRow(
column(4,
fluidRow(
column(6,
box(width = NULL, status = "primary",
radioGroupButtons(inputId = "campcromatph", label = "Numero campionamento", choices = c("1" = "1_campionamento", "2" = "2_campionamento"),
individual = TRUE, checkIcon = list(yes = tags$i(class = "fa fa-circle", style = "color: steelblue"), no = tags$i(class = "fa fa-circle-o", style = "color: steelblue")))
)
),
column(6, box(width=NULL, status = "primary",
selectInput("selyearcromatph", "Seleziona l'anno", choices = "", multiple = FALSE))
)
),
fluidRow(column(12, box(width=NULL, status = "primary", DT::DTOutput("prov3"))))
),
column(8,
column(6, offset = 3,
conditionalPanel(condition = "input.prov3_rows_selected == 0",
box(width = NULL, background = "yellow", tags$i(class = "fas fa-exclamation-triangle", style="font-size: 27px"), h4(strong("Seleziona un'azienda dalla tabella"), style = "color: white"), style = "text-align: justify; text-align: center;")
),
#R1 e olio/posa
conditionalPanel(condition = "input.prov3_rows_selected != 0 && output.check_crompolind == 'no'",
box(width = NULL, background = "yellow", tags$i(class = "fas fa-exclamation-triangle", style="font-size: 27px"), h4(strong("I dati sull'olio e sulla posa riguardano solamente il secondo campionamento."), style = "color: white"), style = "text-align: justify; text-align: center;")
)
),
#non R1 e olio/posa
conditionalPanel(condition = "input.prov3_rows_selected != 0 && output.check_crompolind == 'yes'",
fluidRow(box(width=NULL, status = "primary", title = "Cromatogramma", align= "center", uiOutput("phcromat"))),
fluidRow(
box(width=NULL, status = "primary", title = "Polifenoli",align = "center", style = "overflow-x: scroll;",
DTOutput("tabcromatpolind")
)
)
) #end of conditional panel !=0
) #end of column 8
) #end of fluidRow
)
),
tabPanel(tagList(shiny::icon("map-marked-alt"), HTML(" Mappa")), value = "tabpolindmap",
conditionalPanel(condition = "input.updatepolindmap != 0",
shinycssloaders::withSpinner(tmapOutput("polindmap1"))),
conditionalPanel(condition = "input.addmappolind2 != 0",
hr(),
shinycssloaders::withSpinner(tmapOutput("polindmap2")))
)
)
)
)
), #end of tabitem "inpolsub"
# ####### Tab polifenoli LCxLC ##########
tabItem(tabName = "lcpolsub",
sidebarLayout(
sidebarPanel(width = 2,
radioGroupButtons("selfilepollc", "Seleziona i polifenoli da analizzare",
choiceValues = list("foglie", "drupe", "olio", "posa", "sansa"),
choiceNames = list(
paste(shiny::icon("leaf", style='font-size:16px;'), HTML("<b style=font-size:16px> Foglie</b>")),
paste(tags$img(src = "www/olive_icon2.png", height = "22px", width = "22px"), HTML("<b style=font-size:16px> Drupe</b>")),
paste(tags$img(src = "www/olive_oil.png", height = "22px", width = "22px"), HTML("<b style=font-size:16px> Olio</b>")),
paste(tags$img(src = "www/posa.png", height = "22px", width = "22px"), HTML("<b style=font-size:16px> Posa</b>")),
paste(tags$img(src = "www/sansa3.png", height = "23px", width = "23px"), HTML("<b style=font-size:16px> Sansa</b>"))),
direction = "vertical", justified = TRUE, status = "primary"
),
hr(),
# Tabella
conditionalPanel(condition = "input.tabboxlcxlc == 'tabdtlc'",
awesomeRadio("dttypelc", "Tipo di visualizzazione", choices = c("Wide", "Long"))
),
#Grafici
conditionalPanel(condition = "input.tabboxlcxlc == 'tabgraphlc'",
h4(strong("Impostazioni grafici")),
#scatterplot e barplot
conditionalPanel(condition = "input.boxlcgraph == 'tabpanscattlc' || input.boxlcgraph == 'tabpanbarlc'",
awesomeRadio("lcdatatypescatt", "Filtra i dati per:", choices = c("Azienda", "Polifenolo", "Cultivar principale")),
conditionalPanel(
condition = "input.lcdatatypescatt == 'Azienda'",
selectInput("lcselaziendascatt", "Scegli l'azienda", choices = "")
),
conditionalPanel(
condition = "input.lcdatatypescatt == 'Azienda' || input.lcdatatypescatt == 'Cultivar principale'",
awesomeCheckbox("logscattlc", "Scala logaritmica", value = TRUE)
),
conditionalPanel(
condition = "input.lcdatatypescatt == 'Polifenolo'",
selectInput("lcselpolifscatt", "Scegli il polifenolo", choices = "")
),
conditionalPanel(condition = "input.lcdatatypescatt == 'Cultivar principale'",
selectInput("lcselcultscatt", "Scegli la cultivar principale", choices = ""),
awesomeCheckbox("sintscattlc", "Sintetizza i dati", value = TRUE)
),
selectInput("numscattlc", "Scegli il numero di campionamento", choices = ""),
selectInput("fillscattlc", "Scegli colonna riempimento", choices = "")
),
conditionalPanel(condition = "input.boxlcgraph == 'tabpanbarlc' && input.lcdatatypescatt == 'Cultivar principale'",
awesomeRadio("bartypelc", "Tipo di barplot", choices = c("Affiancato" = "dodge", "Impilato" = "stack")),
selectInput("lcselpolbar", "Polifenoli da mostrare", choices = "")
),
# HEATMAP
conditionalPanel(condition = "input.boxlcgraph == 'tabpanheatlc'",
div(actionButton("updateheatlc", label = "Carica!", class = "btn btn-primary btn-lg", width = "140px", style='padding:5px; font-size:150%; font-weight: bold;'), align= "center"),
br(),
h4(strong("Dati")),
selectInput("numheatlc", "Scegli il numero di campionamento", choices = "", multiple = FALSE),
selectInput("cultheatlc", "Filtra per cultivar", choices = "", multiple = FALSE),
#selectInput("selyearheatmorfo", "Seleziona l'anno", choices = "", multiple = FALSE),
h4(strong("Preprocessing")),
selectInput("selscaleheatlc", "Scala i dati:", choices = c("No" = "none", "Per riga" = "row", "Per colonna" = "column"), selected = "none"),
hr(),
h4(strong("Opzioni dendrogramma")),
###voglio il dendrograma su riga o colonna o entrambi?
h5(strong("Scegli dove mostrare il dendrogramma")),
fluidRow(
column(6, materialSwitch(inputId = "rowdendlc", label = "Riga", value = TRUE, status = "primary", width = "90%")),
column(6, materialSwitch(inputId = "columndendlc", label = "Colonna", value = TRUE, status = "primary", width = "90%"))
),
selectInput("selectannotlc", "Colonna annotazione:", choices = c("Provincia", "Cultivar_principale")),
conditionalPanel(condition = "input.rowdendlc == 1 || input.columndendmorfo == 1",
selectInput("seldistheatlc", "Funzione di distanza:", choices = c("euclidean", "maximum", "manhattan", "canberra", "minkowski"), selected = "euclidean"),
selectInput("selhclustheatlc", "Metodo clustering:", choices = c("ward.D", "ward.D2", "single", "complete", "average" , "mcquitty", "median", "centroid"), selected = "complete"),
),
conditionalPanel(condition = "input.rowdendlc == 0",
h5(strong("Ordinare i dati per annotazione?")),
awesomeCheckbox("heatsortlc", label = "Ordina", value = TRUE)
),
conditionalPanel(condition = "input.rowdendlc == 1",
hr(),
h4(strong("Dendrogramma su riga")),
sliderInput("sliderrowheatlc", "Numero cluster:", min = 2, max = 10, value = 2),
),
conditionalPanel(condition = "input.columndendlc == 1",
hr(),
h4(strong("Dendrogramma su colonna")),
uiOutput("slidercolheatlc"),
)
)
), #end of conditionalpanel grafici
# PCA
conditionalPanel(condition = "input.tabboxlcxlc == 'tabpcalc'",
#selectInput("selyearpca", "Seleziona l'anno", choices = "", multiple = FALSE),
selectInput("numcamppcalc", "Scegli il numero di campionamento", choices = "", multiple = FALSE),
awesomeCheckbox("scalepcalc", "Scala i dati", value = TRUE)
)
), #end of sidebarpanel
mainPanel(width=10,
tabBox(id = "tabboxlcxlc", width=NULL,
tabPanel(tagList(shiny::icon("table"), HTML(" Tabella")), value = "tabdtlc",
box(width = NULL, status = "primary", style = "overflow-x: scroll;",
DT::DTOutput("dtlcxlc")),
mod_render_NAbox_ui("naboxlc")
),
### Galleria
tabPanel(tagList(shiny::icon("images"), HTML(" Galleria")), value = "tablccroma",
fluidPage(
fluidRow(
column(4,
fluidRow(
column(6,
box(width = NULL, status = "primary",
radioGroupButtons("ncampcromatlc", "Numero campionamento", choices = c("1" = "1_campionamento", "2" = "2_campionamento"),
individual = TRUE, checkIcon = list(yes = tags$i(class = "fa fa-circle", style = "color: steelblue"), no = tags$i(class = "fa fa-circle-o", style = "color: steelblue")))
)
)
),
fluidRow(column(12, box(width=NULL, status = "primary", style = "overflow-x: scroll;", DT::DTOutput("dtfotolc"))))
),
conditionalPanel(condition = "input.dtfotolc_rows_selected == 0",
p(strong(h4("Per favore seleziona un'azienda dalla tabella", align = "center")))
),
conditionalPanel(condition = "input.dtfotolc_rows_selected != 0",
column(8,
fluidRow(
box(width=NULL, status = "primary", title = "Cromatogramma", align= "center", uiOutput("phcromatlc"))
),
fluidRow(
column(10, offset = 1,
box(width=NULL, status = "primary",title = "Polifenoli",align = "center",
DTOutput("poliffotolc"))
)
)
)
)
) #end of fluidRow
)
), #end of tabpanel Galleria
##### Grafici
tabPanel(tagList(shiny::icon("chart-bar"), HTML(" Grafici")), value = "tabgraphlc",
tabsetPanel(id = "boxlcgraph",
tabPanel("Scatter plot", value = "tabpanscattlc",
shinycssloaders::withSpinner(image = "www/running_olive.gif", plotly::plotlyOutput("scatterlc", height = "550px"))
),
#barplot
tabPanel("Barplot", value = "tabpanbarlc",
shinycssloaders::withSpinner(image = "www/running_olive.gif", plotly::plotlyOutput("barplotlc", height = "550px"))
),
tabPanel("Heatmap", value = "tabpanheatlc",
br(),
InteractiveComplexHeatmap::InteractiveComplexHeatmapOutput("heatmap_lc_output", layout = "1|(2-3)", width1 = 1150, height1 = 700)
)
)
), # end of tabpanel grafici
###### PCA
tabPanel(tagList(shiny::icon("chart-line"), HTML(" PCA")), value = "tabpcalc",
tabsetPanel(
tabPanel("Plot",
br(),
fluidPage(
fluidRow(
column(3,box(width = NULL, status = "primary",
awesomeRadio("selbiplotlc", "Seleziona tipo di grafico", choices = c("Biplot", "Plot"))
)),
column(4, box(width = NULL, status = "primary",
selectInput("colbiplotlc", "Seleziona colonna riempimento", choices = c("Codice_azienda", "Cultivar_principale", "Areale", "Provincia")))),
column(4, box(width = NULL, status = "primary",
awesomeCheckboxGroup("shpbiplotlc", "Aggiungi geometria", choices = "Provincia", inline = TRUE)
))
),
shinycssloaders::withSpinner(image = "www/running_olive.gif", plotly::plotlyOutput("biplotlc", height = "500px")))
),
tabPanel("Screeplot",
br(),
shinycssloaders::withSpinner(image = "www/running_olive.gif", plotly::plotlyOutput("screeplotlc", width = "75%"))
),
tabPanel("Loadings",
br(),
fluidPage(
fluidRow(column(4, box(width = NULL, status = "primary", uiOutput("sliderpclc")))),
shinycssloaders::withSpinner(image = "www/running_olive.gif", plotly::plotlyOutput("loadingslc", height = "550px")))
),
tabPanel("Plot 3D",
br(),
fluidPage(
fluidRow(
column(4, box(width = NULL, status = "primary",
selectInput("col3dlc", "Seleziona colonna riempimento", choices = c("Codice_azienda", "Provincia", "Cultivar_principale", "Areale"))))
),
shinycssloaders::withSpinner(image = "www/running_olive.gif", plotly::plotlyOutput("pca3dlc", height = "500px")))
)
) #end of tabsetpanel
) #end of tabpanel PCA
) #end of tabbox
) #end of mainpanel
)
), #end of tabitem "lcpolsub"
##### Tab morfometria #####
tabItem(tabName = "anmorfosub",
sidebarLayout(
sidebarPanel(width = 2,
radioGroupButtons("selfilemorfo", "Seleziona la morfometria da analizzare",
choiceValues = list("foglie", "drupe", "endocarpo", "rapporti"),
choiceNames = list(
paste(shiny::icon("leaf", style='font-size:16px;'), HTML("<b style=font-size:16px> Foglie</b>")),
paste(tags$img(src = "www/olive_icon2.png", height = "22px", width = "22px"), HTML("<b style=font-size:16px> Drupe</b>")),
paste(tags$img(src = "www/seed_icon2.png", height = "20px", width = "20px"), HTML("<b style=font-size:16px> Endocarpo</b>")),
paste(tags$img(src = "www/ratio_icon2.png", height = "19px", width = "19px"), HTML("<b style=font-size:16px> Rapporti</b>"))),
direction = "vertical", justified = TRUE, status = "primary"
),
hr(),
# Tabella
conditionalPanel(condition = "input.tabboxmorfo == 'tabdtmor'",
h4(strong("Parametri sintesi")),
selectInput("selyeardtmorfo", "Seleziona l'anno", choices = "", multiple = TRUE),
numericInput("selroundmorfo", value = 3,
label = tags$span("Numero di cifre decimali",
tags$i(class = "glyphicon glyphicon-info-sign", style = "color:#0072B2;",
title = "Scegli quante cifre decimali mostrare nella tabella."))
),
hr(),
materialSwitch(inputId = "summarizetab",
label = tags$span(
"Sintetizza i dati",
tags$i(
class = "glyphicon glyphicon-info-sign",
style = "color:#0072B2;",
title = "Attenzione! Sintetizzando i dati verranno perse le informazioni
sulla classificazione IOC."
)),
value = TRUE, status = "primary"),
conditionalPanel(condition = "input.summarizetab == true",
awesomeCheckboxGroup("selectdtmorfo",
label = tags$span(
"Seleziona la colonna da usare per la sintesi",
tags$i(class = "glyphicon glyphicon-info-sign", style = "color:#0072B2;",
title = "La variabile per cui sintetizzare i dati.
Esempio: con 'Codice_azienda' le misure di ogni azienda sono mediate e si avrà una sola riga per ogni azienda,
mentre se si seleziona 'Cultivar_principale' e 'Provincia' la sintesi è eseguita per queste due variabili
e, dunque, si avranno cinque valori per ogni cultivar, uno per provincia (es. Ravece-SA, Ravece-AV...). Aggiungendo
'Anno', le misure tra i vari anni non verranno mediate ma rimarranno separate.")),
choices = c("Codice_azienda", "Provincia", "Azienda", "Cultivar_principale", "Anno"), selected = c("Codice_azienda", "Anno"))
)
),
# Grafici
conditionalPanel(condition = "input.tabboxmorfo == 'tabpanmorfograph'",
h4(strong("Impostazioni grafici")),
#boxplot e barplot
conditionalPanel(
condition = "input.boxmorfograph == 'tabpanboxmorfo' || input.boxmorfograph == 'tabpanbarmorfo'",
selectInput("selectxmorfobb", "Seleziona la colonna X", choices = c("Codice_azienda", "Provincia", "Azienda", "Cultivar_principale"), multiple = FALSE),
selectInput("selectymorfobb", "Seleziona la colonna Y", choices = "", multiple = FALSE),
selectInput("selectfillmorfobb", "Colonna da usare come riempimento", choices = c("Codice_azienda", "Provincia", "Azienda", "Cultivar_principale"), multiple = FALSE)
),
conditionalPanel(
"input.boxmorfograph == 'tabpanbarmorfo'",
checkboxGroupInput("selyearbarmorfo", "Seleziona anno", choices = "")
),
#scatterplot
conditionalPanel(
condition = "input.boxmorfograph == 'tabpanscattmorfo'",
materialSwitch(inputId = "summarizescatt", label = "Sintetizza i dati", value = TRUE, status = "primary"),
conditionalPanel(condition = "input.summarizescatt == true",
selectInput("selectsummscatt", "Seleziona la colonna da usare per la sintesi", choices = c("Codice_azienda", "Provincia", "Azienda", "Cultivar_principale", "Anno"),
selected = c("Codice_azienda","Anno"), multiple = TRUE),
hr(),
),
selectInput("selectxmorfoscatt", "Seleziona la colonna X", choices = "", multiple = FALSE),
selectInput("selectymorfoscatt", "Seleziona la colonna Y", choices = "", multiple = FALSE),
selectInput("selectfillmorfoscatt", "Colonna da usare come riempimento", choices = "", multiple = FALSE)
),
#IOC
conditionalPanel(
condition = "input.boxmorfograph == 'tabpaniocmorfo'",
radioButtons("selplotioc", label = h4("Tipo di grafico"), choices = list("Grafico a torta" = 1, "Grafico a barre" = 2), selected = 2),
selectInput("selectfillmorfoioc", "Misura IOC", choices = "", multiple = FALSE),
conditionalPanel(condition = "input.selplotioc == 2",
selectInput("selectxmorfoioc", "Seleziona la colonna X", choices = c("Codice_azienda", "Provincia", "Azienda", "Cultivar_principale"), multiple = FALSE),
awesomeRadio("iocselfreq", "Frequenza", choices = c("Frequenza assoluta", "Frequenza relativa"))
),
div(actionButton("addiocmorfo2", label = "Aggiungi secondo grafico"), align = "center"),
conditionalPanel(condition = "input.addiocmorfo2 != 0",
br(),
radioButtons("selplotioc2", label = h4("Tipo di grafico"), choices = list("Grafico a torta" = 1, "Grafico a barre" = 2), selected = 2),
selectInput("selectfillmorfoioc2", "Misura IOC", choices = "", multiple = FALSE),
conditionalPanel(condition = "input.selplotioc2 == 2",
selectInput("selectxmorfoioc2", "Seleziona la colonna X", choices = c("Codice_azienda", "Provincia", "Azienda", "Cultivar_principale"), multiple = FALSE),
awesomeRadio("iocselfreq2", "Frequenza", choices = c("Frequenza assoluta", "Frequenza relativa"))
)
)
),
# HEATMAP
conditionalPanel(
condition = "input.boxmorfograph == 'tabpanheatmorfo'",
div(actionButton("updateheatmorfo", label = "Carica!", class = "btn btn-primary btn-lg", width = "140px", style='padding:5px; font-size:150%; font-weight: bold;'), align= "center"),
br(),
h4(strong("Dati")),
selectInput("numheatmorfo", "Scegli il numero di campionamento", choices = "", multiple = FALSE),
selectInput("selyearheatmorfo", "Seleziona l'anno", choices = "", multiple = FALSE),
hr(),
h4(strong("Opzioni dendrogramma")),
###voglio il dendrograma su riga o colonna o entrambi?
h5(strong("Scegli dove mostrare il dendrogramma")),
fluidRow(
column(6, materialSwitch(inputId = "rowdendmorfo", label = "Riga", value = TRUE, status = "primary", width = "90%")),
column(6, materialSwitch(inputId = "columndendmorfo", label = "Colonna", value = TRUE, status = "primary", width = "90%"))
),
selectInput("selectannotmorfo", "Colonna annotazione:", choices = c("Provincia", "Cultivar_principale")),
conditionalPanel(condition = "input.rowdendmorfo == 1 || input.columndendmorfo == 1",
selectInput("seldistheatmorfo", "Funzione di distanza:", choices = c("euclidean", "maximum", "manhattan", "canberra", "minkowski"), selected = "euclidean"),
selectInput("selhclustheatmorfo", "Metodo clustering:", choices = c("ward.D", "ward.D2", "single", "complete", "average" , "mcquitty", "median", "centroid"), selected = "complete"),
),
conditionalPanel(condition = "input.rowdendmorfo == 0",
h5(strong("Ordinare i dati per annotazione?")),
awesomeCheckbox("heatsortmorfo", label = "Ordina", value = TRUE)
),
conditionalPanel(condition = "input.rowdendmorfo == 1",
hr(),
h4(strong("Dendrogramma su riga")),
sliderInput("sliderrowheatmorfo", "Numero cluster:", min = 2, max = 10, value = 2),
),
conditionalPanel(condition = "input.columndendmorfo == 1",
hr(),
h4(strong("Dendrogramma su colonna")),
uiOutput("sliderheatcolmorfo"),
)
),
conditionalPanel(condition = "input.boxmorfograph == 'tabpancorrmorfo'",
selectInput("selyearcorrmorfo", "Seleziona l'anno", choices = "", multiple = FALSE)
)
), #end of conditionapanel dei grafici
# PCA
conditionalPanel(
condition = "input.tabboxmorfo == 'tabpcamor'",
selectInput("selyearpcamorfo", "Seleziona l'anno", choices = "", multiple = FALSE),
selectInput("numpcamorfo", "Scegli il numero di campionamento", choices = "", multiple = FALSE),
materialSwitch(inputId = "summarizepcamorfo", label = "Sintetizza i dati", value = TRUE, status = "primary"),
radioGroupButtons(inputId = "selcorpcamorfo", label = "Matrice:", choices = c("Correlazione" = TRUE, "Covarianza" = FALSE),
individual = TRUE, checkIcon = list(yes = tags$i(class = "fa fa-circle", style = "color: steelblue"),no = tags$i(class = "fa fa-circle-o", style = "color: steelblue")))
),
# Clustering
conditionalPanel(
condition = "input.tabboxmorfo == 'tabclustmor'",
selectInput("selcolclustmorfo", "Seleziona variabile", choices = c("Codice_azienda", "Cultivar_principale")),
selectInput("selyearclustmorfo", "Seleziona l'anno", choices = "", multiple = TRUE),
selectInput("numclustmorfo", "Scegli il numero di campionamento", choices = "", multiple = FALSE),
#materialSwitch(inputId = "summarizeclustmorfo", label = "Sintetizza i dati", status = "primary", value = TRUE),
radioGroupButtons("selclustmethod", "Tipo di clustering", choices = c("Gerarchico", "Partizionale"), justified = TRUE, status = "primary"),
conditionalPanel(
condition = "input.selclustmethod == 'Partizionale'",
selectInput("selclusthmorfo", "Seleziona l'algoritmo di clustering", choices = c("K-means", "PAM", "Clara"), selected = "K-means", multiple = FALSE),
)
),
#Test d'ipotesi
conditionalPanel(condition = "input.tabboxmorfo == 'tabpanmorfotest'",
h4(strong("Opzioni test")),
selectInput("selyearttestmorfo", "Scegli l'anno", choices = "", multiple = TRUE),
hr(),
#T-test
conditionalPanel(condition = "input.boxmorfotest == 'tabpanttestmorfo'",
selectInput("catvarttest", "Variabile categorica", choices = "", multiple = FALSE),
selectInput("culttest1", "Variabile dipendente", choices = "", multiple = FALSE),
selectInput("culttest2", "Fattore esplicativo", choices = "", multiple = FALSE),
selectInput("numvarttest", "Variabile numerica da confrontare", choices = "", multiple = FALSE),
awesomeRadio("selectttest", "Tipo di test", choices = c("T-test", "Wilcoxon-Mann-Whitney")),
conditionalPanel(condition = "input.selectttest == 'T-test'",
awesomeCheckbox("selvarequal", "Omoschedasticità", value = TRUE)
)
),
#Test correlazione
conditionalPanel(
condition = "input.boxmorfotest == 'tabpancorrtestmorfo'",
selectInput("corrtest1", "Variabile dipendente", choices = "", multiple = FALSE),
selectInput("corrtest2", "Fattore esplicativo", choices = "", multiple = FALSE),
awesomeRadio("selectcorrtest", "Tipo di test", choices = c("Pearson" = "pearson", "Kendall" = "kendall", "Spearman" = "spearman")),
hr(),
selectInput("corrtestfill", "Colonna riempimento", choices = "", multiple = FALSE),
awesomeCheckbox("numfitcorrtest", "Singolo fit", value = TRUE),
awesomeCheckbox("selsecorrtest", "Intervallo di confidenza", value = TRUE),
),
#Test indipendenza
conditionalPanel(
condition = "input.boxmorfotest == 'tabpanchisqtestmorfo'",
selectInput("chisqtest1", "Variabile descrittiva", choices = c("Codice_azienda", "Provincia", "Cultivar_principale"), multiple = FALSE, selected = "Cultivar_principale"),
selectInput("chisqtest2", "Variabile categorica", choices = "", multiple = FALSE),
awesomeRadio("selectchisqtest", "Tipo di test", choices = c("Test esatto di Fisher", "Test d'indipendenza Chi-quadro")),
awesomeCheckbox("simulatechisq", "Simulazione p-value (Monte Carlo)", value = TRUE),
awesomeRadio("pvalchisqmorfo", "Livello di significatività", choices = c(0.01, 0.05, 0.1), selected = 0.05),
selectInput("chisqtestfilt", "Filtrare i dati (opzionale)", choices = "", multiple = TRUE)
),
#Test Anova
conditionalPanel(condition = "input.boxmorfotest == 'tabpananovamorfo'",
awesomeRadio("selectanovatest", "Tipo di test", choices = c("One-way ANOVA", "Two-way ANOVA")),
conditionalPanel(condition = "input.selectanovatest == 'One-way ANOVA'",
awesomeRadio("selectanovatest2", "Tipo di test", choices = c("ANOVA", "Kruskal-Wallis")),
),
awesomeRadio("pvalanovamorfo", "Livello di significatività", choices = c(0.01, 0.05, 0.1), selected = 0.05),
selectInput("anovanum", "Variabile numerica", choices = "", multiple = FALSE),
selectInput("anovacat", "Variabile categorica", choices = "", multiple = FALSE),
conditionalPanel(condition = "input.selectanovatest == 'Two-way ANOVA'",
selectInput("anovacat2", "Seconda variabile categorica", choices = "", multiple = FALSE),
awesomeRadio("anova2typemorfo", "Tipo di ANOVA", choices = c("Modello additivo", "Modello con interazione"))
)
),
),
# Mappa
conditionalPanel(
condition = "input.tabboxmorfo == 'tabmapmor'",
div(actionButton("upmapmorfo", "Carica mappa", class = "btn-primary", style = 'padding:4px; font-size:160%'), align = "center"),
conditionalPanel(
condition = ("input.upmapmorfo != 0"),
br(),
selectInput("mapxmorfomap1", "Seleziona la colonna da visualizzare", choices = "", multiple = FALSE),
selectInput("selyearmorfomap1", "Seleziona l'anno", choices = "", multiple = FALSE),
selectInput("nummorfomap1", "Scegli il numero di campionamento", choices = "", multiple = FALSE),
div(actionButton("addmapmorfo2", label = "Aggiungi seconda mappa"), align = "center"),
conditionalPanel(
condition = ("input.addmapmorfo2 != 0"),
br(),
selectInput("mapxmorfomap2", "Seleziona la colonna da visualizzare", choices = "", multiple = FALSE),
selectInput("selyearmorfomap2", "Seleziona l'anno", choices = "", multiple = FALSE),
selectInput("nummorfomap2", "Scegli il numero di campionamento", choices = "", multiple = FALSE)
)
)
)
), #end of sidebarpanel
#### mainpanel ####
mainPanel(width = 10,
tabBox(id = "tabboxmorfo", width=NULL,
tabPanel(tagList(shiny::icon("table"), HTML(" Tabella")), value = "tabdtmor",
fluidPage(
fluidRow(box(width = 12, status = "primary", style = "overflow-x: scroll;",
DT::DTOutput("dtmorfo"))),
mod_render_NAbox_ui("naboxmorfo")
)
),
tabPanel(tagList(shiny::icon("images"), HTML(" Galleria")), value = "tabmorfomor",
fluidPage(
fluidRow(
column(width=4,
fluidRow(
column(6, box(width = NULL, status = "primary",
radioGroupButtons(
inputId = "campfotomorfo", label = "Numero campionamento",
choices = c("1" = "1_campionamento", "2" = "2_campionamento"), individual = TRUE,
checkIcon = list(yes = tags$i(class = "fa fa-circle", style = "color: steelblue"),
no = tags$i(class = "fa fa-circle-o", style = "color: steelblue"))
))
),
column(6, box(width=NULL, status = "primary",
selectInput("selyearfotomorfo", "Seleziona l'anno", choices = "", multiple = FALSE))
)
),
fluidRow(column(12, box(width=NULL, status = "primary", style = "overflow-x: scroll;", DT::DTOutput("dtfotomorfo"))))
),
column(width = 8,
column(width = 6, offset = 3,
conditionalPanel(condition = "input.dtfotomorfo_rows_selected == 0",
box(width = NULL, background = "yellow", tags$i(class = "fas fa-exclamation-triangle", style="font-size: 27px"), h4(strong("Seleziona un'azienda dalla tabella"), style = "color: white"), style = "text-align: justify; text-align: center;"),
),
conditionalPanel(condition = "input.dtfotomorfo_rows_selected != 0 && input.campfotomorfo == '1_campionamento'",
box(width = NULL, background = "yellow", tags$i(class = "fas fa-exclamation-triangle", style="font-size: 27px"), h4(strong("Nessuna foto in archivio. I dati sulla morfometria riguardano solamente il secondo campionamento."), style = "color: white"), style = "text-align: justify; text-align: center;"),
)
),
conditionalPanel(
condition = "input.dtfotomorfo_rows_selected != 0 && input.campfotomorfo == '2_campionamento'",
uiOutput("phmorfo")
)
)
) #end of fluidRow
)
), #end of tabpanel Foto
tabPanel(tagList(shiny::icon("chart-bar"), HTML(" Grafici")), value = "tabpanmorfograph",
tabsetPanel(id = "boxmorfograph",
tabPanel("Boxplot", value = "tabpanboxmorfo",
shinycssloaders::withSpinner(image = "www/running_olive.gif", plotly::plotlyOutput("boxmorfo"))
),
tabPanel("Barplot", value = "tabpanbarmorfo",
shinycssloaders::withSpinner(image = "www/running_olive.gif", plotly::plotlyOutput("barmorfo"))
),
tabPanel("Scatter plot", value = "tabpanscattmorfo",
shinycssloaders::withSpinner(image = "www/running_olive.gif", plotly::plotlyOutput("scattmorfo"))
),
tabPanel("IOC", value = "tabpaniocmorfo",
shinycssloaders::withSpinner(image = "www/running_olive.gif", plotly::plotlyOutput("iocmorfo")),
conditionalPanel(condition = "input.addiocmorfo2 != 0",
hr(),
shinycssloaders::withSpinner(image = "www/running_olive.gif", plotly::plotlyOutput("iocmorfo2")),
)
),
tabPanel("Heatmap", value = "tabpanheatmorfo",
br(),
InteractiveComplexHeatmap::InteractiveComplexHeatmapOutput("heatmap_morfo_output", layout = "1|(2-3)", width1 = 850, height1 = 600)
),
tabPanel("Correlation plot", value = "tabpancorrmorfo",
br(),
shinycssloaders::withSpinner(image = "www/running_olive.gif", plotly::plotlyOutput("corrplotmorfo"))
)
)
),
#pca
tabPanel(tagList(shiny::icon("chart-line"), HTML(" PCA")), value = "tabpcamor",
tabsetPanel(
tabPanel("Plot",
br(),
fluidPage(
fluidRow(
column(3, box(width = NULL, status = "primary",
awesomeRadio("selbiplotmorfo", "Seleziona tipo di grafico", choices = c("Biplot", "Plot")))),
column(3, box(width = NULL, status = "primary",
selectInput("colbiplotmorfo", "Seleziona colonna riempimento", choices = c("Codice_azienda", "Provincia", "Cultivar_principale", "Areale")))),
column(3, box(width = NULL, status = "primary",
awesomeCheckboxGroup(inputId = "shpbiplotmorfo", label = "Aggiungi geometria", choices = "Provincia", inline = TRUE)
))
),
shinycssloaders::withSpinner(image = "www/running_olive.gif", plotly::plotlyOutput("biplotmorfo", height = "500px")))
),
tabPanel("Screeplot",
br(),
shinycssloaders::withSpinner(image = "www/running_olive.gif", plotly::plotlyOutput("screeplotmorfo", width = "75%"))
),
tabPanel("Loadings",
br(),
fluidPage(
fluidRow(column(4, box(width = NULL, status = "primary",
uiOutput("sliderpcmorfo")))),
shinycssloaders::withSpinner(image = "www/running_olive.gif", plotly::plotlyOutput("loadingsmorfo")))
),
tabPanel("Plot 3D",
br(),
fluidPage(
fluidRow(
column(4, box(width = NULL, status = "primary",
selectInput("col3dmorfo", "Seleziona colonna riempimento", choices = c("Codice_azienda", "Provincia", "Cultivar_principale", "Areale"))))
),
shinycssloaders::withSpinner(image = "www/running_olive.gif", plotly::plotlyOutput("pca3dmorfo", height = "500px")))
)
)
), #end of tabpanel PCA
# Clustering
tabPanel(tagList(tags$img(src = "www/clustering_icon.png", height = "16px", width = "16px"), HTML(" Clustering")), value = "tabclustmor",
tabsetPanel(
tabPanel("Cluster plot",
br(),
fluidPage(
fluidRow(
column(4,
box(width = NULL, status = "primary",
sliderInput("selnumclustmorfo", "Numero cluster:", min = 1, max = 10, value = 2))),
column(4,
conditionalPanel(condition = "input.selclustmethod == 'Gerarchico'",
box(width=NULL, status = "primary",
selectInput("selhclustmeth", "Seleziona metodo agglomerazione", choices = c("single", "complete", "ward.D", "ward.D2"), selected = "ward.D2"))
)
)
),
shinycssloaders::withSpinner(image = "www/running_olive.gif", plotOutput("plotclustermorfo", height = "600px"))
)
),
tabPanel("Numero cluster",
br(),
shinycssloaders::withSpinner(image = "www/running_olive.gif", plotOutput("numclustergraph", height = "800px"))
)
)
), #end of tabpanel clustering
#tabpanel test d'ipotesi
tabPanel(tagList(shiny::icon("clipboard-check"), HTML(" Test d'ipotesi")), value = "tabpanmorfotest",
tabsetPanel(id = "boxmorfotest",
# Test di correlazione
tabPanel("Test di correlazione", value = "tabpancorrtestmorfo",
br(),
fluidPage(
fluidRow(
column(6, box(width = NULL, title = strong("Test sulla normalità"), status = "primary", verbatimTextOutput("shapirocorr1"))),
column(6, box(width = NULL, title = strong("Test sulla normalità"), status = "primary", verbatimTextOutput("shapirocorr2")))
),
fluidRow(
column(6,
conditionalPanel(condition = "input.corrtest1 != input.corrtest2",
box(width = NULL, title = strong("Test statistico"), status = "primary", verbatimTextOutput("corrtest"))),
conditionalPanel(condition = "input.corrtest1 == input.corrtest2",
box(width = NULL, title = strong("Test statistico"), status = "warning", tags$i(class = "fas fa-exclamation-triangle", style="font-size: 20px; color: rgb(243,156,18)"),
h5(strong("Errore. La variabile dipendente e il fattore esplicativo devono essere diversi.", style = "color: rgb(243,156,18)")), style = "text-align: justify; text-align: center;"))
),
column(6, box(width = NULL, title = strong("Grafico"), status = "primary",
shinycssloaders::withSpinner(image = "www/running_olive.gif", plotly::plotlyOutput("scattcorrtest"))))
)
),
), #end of tabpanel
tabPanel("Confronto tra due gruppi", value = "tabpanttestmorfo",
br(),
fluidPage(
fluidRow(
column(6, box(width = NULL, title = strong("Test sulla normalità"), status = "primary", verbatimTextOutput("shapiro1"))),
column(6, box(width = NULL, title = strong("Test sulla normalità"), status = "primary", verbatimTextOutput("shapiro2")))
),
fluidRow(
conditionalPanel(condition = "input.culttest1 != input.culttest2 && (output.shapttestmorfoui == 'distribuzione normale' || input.selectttest == 'Wilcoxon-Mann-Whitney')",
column(6,box(width = NULL, title = strong("Test sulla varianza"), status = "primary", verbatimTextOutput("vartest1"))),
column(6,box(width = NULL, title = strong("Test statistico"), status = "primary", verbatimTextOutput("ttest1")))
),
conditionalPanel(condition = "input.culttest1 == input.culttest2",
column(6, box(width = NULL, title = strong("Test sulla varianza"), status = "warning", tags$i(class = "fas fa-exclamation-triangle", style="font-size: 20px; color: rgb(243,156,18)"),
h5(strong("Errore. La variabile dipendente e il fattore esplicativo devono essere diversi.", style = "color: rgb(243,156,18)")), style = "text-align: justify; text-align: center;")),
column(6, box(width = NULL, title = strong("Test statistico"), status = "warning", tags$i(class = "fas fa-exclamation-triangle", style="font-size: 20px; color: rgb(243,156,18)"),
h5(strong("Errore. La variabile dipendente e il fattore esplicativo devono essere diversi.", style = "color: rgb(243,156,18)")), style = "text-align: justify; text-align: center;"))
),
conditionalPanel(
condition = "input.culttest1 != input.culttest2 && output.shapttestmorfoui == 'distribuzione non normale' && input.selectttest == 'T-test'",
column(6, offset = 3,
box(width = NULL, status = "warning", style = "text-align: justify; text-align: center;", br(),
tags$i(class = "fas fa-exclamation-triangle", style="font-size: 25px; color: rgb(243,156,18)"),
h4(strong("Una o più variabili non seguono una distribuzione normale. Scegli il Wilcoxon-Mann-Whitney test.", style = "color: rgb(243,156,18)")),
br()
)
)
)
),
fluidRow(
column(8, offset = 2, box(width = NULL, title = strong("Grafico"), status = "primary",
shinycssloaders::withSpinner(image = "www/running_olive.gif", plotly::plotlyOutput("boxttest"))))
)
) #end of fluidpage
), #end of tabpanel conf 2 gruppi
# Confronto tra più gruppi
tabPanel("Confronto tra più gruppi", value = "tabpananovamorfo",
fluidPage(
fluidRow(
column(12, box(width = NULL, title = strong("Boxplot"), status = "primary",
shinycssloaders::withSpinner(image = "www/running_olive.gif", plotly::plotlyOutput("boxanova"))))
),
fluidRow(
column(6, box(width = NULL, title = strong("Test sulla normalità"), status = "primary", verbatimTextOutput("shapiroanova1"))),
conditionalPanel(condition = "(output.shapanovamorfoui == 'distribuzione normale' && (input.selectanovatest2 == 'ANOVA' || input.selectanovatest2 == 'Kruskal-Wallis')) || (output.shapanovamorfoui == 'distribuzione non normale' && input.selectanovatest2 == 'Kruskal-Wallis')",
conditionalPanel(condition = "input.selectanovatest2 == 'ANOVA'",
column(6, box(width = NULL, title = strong("Test ANOVA"), status = "primary", verbatimTextOutput("anova1morfoprint")))
),
conditionalPanel(condition = "input.selectanovatest2 == 'Kruskal-Wallis'",
column(6, box(width = NULL, title = strong("Test Kruskal-Wallis"), status = "primary", verbatimTextOutput("kruskmorfo")))
)
),
conditionalPanel(condition = "output.shapanovamorfoui == 'distribuzione non normale' && input.selectanovatest2 == 'ANOVA'",
column(6, box(width = NULL, title = strong("Test ANOVA"), status = "warning", style = "text-align: justify; text-align: center;",
tags$i(class = "fas fa-exclamation-triangle", style="font-size: 25px; color: rgb(243,156,18)"),
h4(strong("La variabile numerica non segue la distribuzione normale. Scegli il test Kruskal-Wallis.", style = "color: rgb(243,156,18)")),
))
)
),
conditionalPanel(condition = "(output.shapanovamorfoui == 'distribuzione normale' && (input.selectanovatest2 == 'ANOVA' || input.selectanovatest2 == 'Kruskal-Wallis')) || (output.shapanovamorfoui == 'distribuzione non normale' && input.selectanovatest2 == 'Kruskal-Wallis')",
fluidRow(
column(10,offset = 1,
box(width = NULL, title = strong("Post-hoc"), status = "primary", style = "text-align: justify; text-align: center;",
conditionalPanel(condition = "output.signiftestmorfoui == 'significativo'",
conditionalPanel(condition = "input.selectanovatest2 == 'ANOVA'",
h4(strong("Tukey HSD"))),
conditionalPanel(condition = "input.selectanovatest2 == 'Kruskal-Wallis'",
h4(strong("Dunn Test")),
),
shinycssloaders::withSpinner(image = "www/running_olive.gif", plotly::plotlyOutput("posthocmorfograph"))
),
conditionalPanel(condition = "output.signiftestmorfoui == 'non significativo'",
tags$i(class = "fas fa-exclamation-triangle", style="font-size: 25px; color: rgb(243,156,18)"),
h4(strong("Il p-value è maggiore del livello di significatività impostato. Non ci sono differenze significative tra le variabili.", style = "color: rgb(243,156,18)"))
)
)
)
) #end of fluidrow post-hoc
)
) #end of fluidpage
), #end of tabpanel più gruppi
#Test d'indipendenza
tabPanel("Test d'indipendenza", value = "tabpanchisqtestmorfo",
br(),
fluidPage(
fluidRow(
column(5, box(width = NULL, title = strong("Tabella di contingenza"), status = "primary", tableOutput("contingtablemorfo"))),
column(6,
fluidRow(
box(width = NULL, title = strong("Test"), status = "primary", verbatimTextOutput("chisqmorfoprint"))
),
fluidRow(
conditionalPanel(condition = "output.signiftestchisqmorfoui == 'significativo'",
#box(width = NULL, title = strong("Grafico residui"), status = "primary", style = "text-align: justify; text-align: center;",
shinycssloaders::withSpinner(image = "www/running_olive.gif", plotOutput("plotresidchisq"))
# )
),
conditionalPanel(condition = "output.signiftestchisqmorfoui == 'non significativo'",
box(width = NULL, status = "warning", style = "text-align: justify; text-align: center;",
tags$i(class = "fas fa-exclamation-triangle", style="font-size: 25px; color: rgb(243,156,18)"),
h4(strong("Il p-value è maggiore del livello di significatività impostato. Le variabili sono indipendenti.", style = "color: rgb(243,156,18)"))
)
)
) #end of fluidrow grafico
)
) #end of first fluidrow
)
)
) #end of tabset panel
),
#tabpanel mappa
tabPanel(tagList(shiny::icon("map-marked-alt"), HTML(" Mappa")), value = "tabmapmor",
conditionalPanel(condition = ("input.upmapmorfo != 0"),
shinycssloaders::withSpinner(tmapOutput("mapmorfo1")),
conditionalPanel(condition = "input.addmapmorfo2 != 0",
hr(),
shinycssloaders::withSpinner(tmapOutput("mapmorfo2"))
)
))
) #end of tabBox
) #end of mainpanel
) #end of sidebarlayout
), #end of tabitem morfo
##### Tab integrazione dati ####
tabItem(
tabName = "integrdati",
sidebarLayout(
sidebarPanel(
width = 2,
h4(strong("Scegli un confronto")),
radioGroupButtons("conf_type1", "Scegli una prima variabile",
choiceValues = list("tot","ind"),
choiceNames = list(
paste(icon("circle"), HTML("<b> Polifenoli totali</b>")),
paste(icon("circle"), HTML("<b> Polifenoli individuali</b>"))
),direction = "vertical", justified = TRUE, status = "primary"),
radioGroupButtons("conf_type2", "Scegli una seconda variabile",
choiceValues = list("camp", "prec", "ind"),
choiceNames = list(
paste(icon("circle"), HTML("<b> Schede campionamento</b>")),
paste(icon("circle"), HTML("<b> Precipitazioni</b>")),
paste(icon("circle"), HTML("<b> Polifenoli individuali</b>"))
),direction = "vertical", justified = TRUE, status = "primary"),
hr(),
selectInput("conf_selpoltot", "Seleziona una misura", choices = c("Foglie", "Drupe", "Olio", "Posa", "Sansa")),
conditionalPanel(
condition = "input.conf_type2 == 'prec'",
selectInput("varmeteo_conf", "Seleziona misura di precipitazione", choices = c("Precipitazioni totali" = "tp",
"Volume d'acqua nel suolo (7-28cm)" = "swvl2",
"Volume d'acqua nel suolo (28-100cm)" = "swvl3"))
),
selectInput("conf_selyear", "Scegli uno o più anni", choices = c("2020", "2021"), multiple = TRUE, selected = "2020"),
conditionalPanel(
condition = "input.tabboxconf == 'tabpan_testconf'",
selectInput("conf_selcamp_test", "Scegli uno o più campionamenti", choices = "", multiple = TRUE)
),
hr(),
#grafici
conditionalPanel(
condition = "input.tabboxconf == 'tabpan_graphconf' && input.boxconfgraph == 'tabgraph_scattconf'",
h4(strong("Impostazioni grafici")),
awesomeRadio("typescatt_conf", "Dati da analizzare", choices = c("Tutti", "Filtra per cultivar")),
conditionalPanel(
condition = "input.typescatt_conf == 'Filtra per cultivar'",
selectInput("selcult_scatt_conf", "Scegli la/le cultivar", choices = "", multiple = TRUE)),
selectInput("scattx_conf", "Seleziona la colonna X", choices = ""),
selectInput("scatty_conf", "Seleziona la colonna Y", choices = ""),
hr(),
h4(strong("Altre opzioni")),
conditionalPanel(
condition = "input.conf_selyear.length > 1",
awesomeCheckbox("scattfacet_conf", "Dividi gli anni in due grafici", value = FALSE)
),
conditionalPanel(
condition = "input.typescatt_conf == 'Filtra per cultivar'",
awesomeCheckbox("scatt_dens_conf", "Density plot 2D", value = FALSE),
fluidRow(
column(4, br(), awesomeCheckbox("scatt_fit_conf", "Fit", value = FALSE)),
conditionalPanel(
condition = "input.scatt_fit_conf == true",
column(8, awesomeRadio("scatt_selmodfit_conf", "Modello fit", choices = c("lm", "loess"),inline = T))
))
)
),
#### TEST d'ipotesi
#Test d'ipotesi
conditionalPanel(
condition = "input.tabboxconf == 'tabpan_testconf'",
h4(strong("Opzioni test")),
#Test correlazione
conditionalPanel(
condition = "input.boxconftest == 'tabpancorrtest_conf'",
selectInput("corrtest1_conf", "Variabile dipendente", choices = "", multiple = FALSE),
selectInput("corrtest2_conf", "Fattore esplicativo", choices = "", multiple = FALSE),
awesomeRadio("selectcorrtest_conf", "Tipo di test", choices = c("Pearson" = "pearson", "Kendall" = "kendall", "Spearman" = "spearman")),
hr(),
selectInput("corrtestfill_conf", "Colonna riempimento", choices = "", multiple = FALSE),
awesomeCheckbox("numfitcorrtest_conf", "Singolo fit", value = TRUE),
awesomeCheckbox("selsecorrtest_conf", "Intervallo di confidenza", value = TRUE),
awesomeRadio("selmod_fit_conf", "Seleziona un metodo per il fit", choices = c("lm", "loess", "auto"))
),
#T-test
conditionalPanel(
condition = "input.boxconftest == 'tabpanttest_conf'",
selectInput("catvarttest_conf", "Variabile categorica", choices = "", multiple = FALSE),
selectInput("culttest1_conf", "Variabile dipendente", choices = "", multiple = FALSE),
selectInput("culttest2_conf", "Fattore esplicativo", choices = "", multiple = FALSE),
selectInput("numvarttest_conf", "Variabile numerica da confrontare", choices = "", multiple = FALSE),
awesomeRadio("selectttest_conf", "Tipo di test", choices = c("T-test", "Wilcoxon-Mann-Whitney")),
conditionalPanel(condition = "input.selectttest_conf == 'T-test'",
awesomeCheckbox("selvarequal_conf", "Omoschedasticità", value = TRUE)
)
),
#Test Anova
conditionalPanel(
condition = "input.boxconftest == 'tabpananova_conf'",
awesomeRadio("selectanovatest_conf", "Tipo di test", choices = c("One-way ANOVA", "Two-way ANOVA")),
conditionalPanel(
condition = "input.selectanovatest_conf == 'One-way ANOVA'",
awesomeRadio("selectanovatest2_conf", "Tipo di test", choices = c("ANOVA", "Kruskal-Wallis")),
),
awesomeRadio("pvalanovamorfo_conf", "Livello di significatività", choices = c(0.01, 0.05, 0.1), selected = 0.05),
selectInput("anovanum_conf", "Variabile numerica", choices = "", multiple = FALSE),
selectInput("anovacat_conf", "Variabile categorica", choices = "", multiple = FALSE),
conditionalPanel(condition = "input.selectanovatest_conf == 'Two-way ANOVA'",
selectInput("anovacat2_conf", "Seconda variabile categorica", choices = "", multiple = FALSE),
awesomeRadio("anova2typemorfo_conf", "Tipo di ANOVA", choices = c("Modello additivo", "Modello con interazione"))
)
)
#
# #Test indipendenza
# conditionalPanel(
# condition = "input.boxmorfotest == 'tabpanchisqtestmorfo'",
# selectInput("chisqtest1", "Variabile descrittiva", choices = c("Codice_azienda", "Provincia", "Cultivar_principale"), multiple = FALSE, selected = "Cultivar_principale"),
# selectInput("chisqtest2", "Variabile categorica", choices = "", multiple = FALSE),
# awesomeRadio("selectchisqtest", "Tipo di test", choices = c("Test esatto di Fisher", "Test d'indipendenza Chi-quadro")),
# awesomeCheckbox("simulatechisq", "Simulazione p-value (Monte Carlo)", value = TRUE),
# awesomeRadio("pvalchisqmorfo", "Livello di significatività", choices = c(0.01, 0.05, 0.1), selected = 0.05),
# selectInput("chisqtestfilt", "Filtrare i dati (opzionale)", choices = "", multiple = TRUE)
#
#
# ),
#
)
),
mainPanel(width = 10,
tabBox(id = "tabboxconf", width = NULL,
###tabella
tabPanel(tagList(icon("table"), HTML(" Tabella")), value = "tabpan_tableconf",
fluidPage(box(width=12, status = "primary", style = "overflow-x: scroll;", DT::DTOutput("dt_conf"))),
downloadButton("down_integrazione", "Download dati")
),
##### confronti grafici ####
tabPanel(
tagList(icon("chart-bar"), HTML(" Grafici")), value = "tabpan_graphconf",
tabsetPanel(
id = "boxconfgraph",
tabPanel(
"Scatter plot", value = "tabgraph_scattconf",
fluidPage(
box(width=NULL, status = "primary",
fluidRow(
column(3, selectInput("scattnum_conf", "Scegli il numero di campionamento", choices = "", multiple = TRUE)),
column(3, selectInput("scattfill_conf", "Colonna da usare come riempimento", choices = "", multiple = FALSE)),
column(3, selectInput("scattsize_conf", "Colonna da usare come dimensione", choices = "")),
column(3, selectInput("scattshape_conf", "Colonna da usare come forma", choices = ""))
)),
plotly::plotlyOutput("scatterconf",height = "100%"),
)
),
tabPanel(
"Correlation plot", value = "tabgraph_corrconf",
fluidPage(
box(width=NULL, status = "primary",
fluidRow(
column(3, selectInput("corrnum_conf", "Scegli il numero di campionamento", choices = "", multiple = TRUE)),
)),
plotly::plotlyOutput("corrplotconf")
)
)
) #end tabset boxconfgraph
), #end of tabpanel grafici
#####mainpanel test d'ipotesi
#tabpanel test d'ipotesi
tabPanel(
tagList(
icon("clipboard-check"), HTML(" Test d'ipotesi")), value = "tabpan_testconf",
tabsetPanel(
id = "boxconftest",
# Test di correlazione
tabPanel(
"Test di correlazione", value = "tabpancorrtest_conf",
conditionalPanel(
condition = "input.conf_type2 == 'camp'",
br(),
fluidPage(helpText("Test di correlazione non disponibile per questo tipo di confronto"))
),
conditionalPanel(
condition = "input.conf_type2 != 'camp'",
br(),
fluidPage(
fluidRow(
column(6, box(width = NULL, title = strong("Test sulla normalità"), status = "primary", verbatimTextOutput("shapirocorr1_conf"))),
column(6, box(width = NULL, title = strong("Test sulla normalità"), status = "primary", verbatimTextOutput("shapirocorr2_conf")))
),
fluidRow(
column(
6,
conditionalPanel(condition = "input.corrtest1_conf != input.corrtest2_conf",
box(width = NULL, title = strong("Test statistico"), status = "primary", verbatimTextOutput("corrtest_conf"))),
conditionalPanel(condition = "input.corrtest1_conf == input.corrtest2_conf",
box(width = NULL, title = strong("Test statistico"), status = "warning", tags$i(class = "fas fa-exclamation-triangle", style="font-size: 20px; color: rgb(243,156,18)"),
h5(strong("Errore. La variabile dipendente e il fattore esplicativo devono essere diversi.", style = "color: rgb(243,156,18)")), style = "text-align: justify; text-align: center;"))
),
column(6, box(width = NULL, title = strong("Grafico"), status = "primary",
shinycssloaders::withSpinner(image = "www/running_olive.gif", plotly::plotlyOutput("scattcorrtest_conf"))))
)
)
)
), #end of tabpanel
tabPanel(
"Confronto tra due gruppi", value = "tabpanttest_conf",
br(),
fluidPage(
fluidRow(
column(6, box(width = NULL, title = strong("Test sulla normalità"), status = "primary", verbatimTextOutput("shapiro1_conf"))),
column(6, box(width = NULL, title = strong("Test sulla normalità"), status = "primary", verbatimTextOutput("shapiro2_conf")))
),
fluidRow(
conditionalPanel(
condition = "input.culttest1_conf != input.culttest2_conf && (output.shapttestmorfoui_conf == 'distribuzione normale' || input.selectttest_conf == 'Wilcoxon-Mann-Whitney')",
column(6,box(width = NULL, title = strong("Test sulla varianza"), status = "primary", verbatimTextOutput("vartest1_conf"))),
column(6,box(width = NULL, title = strong("Test statistico"), status = "primary", verbatimTextOutput("ttest1_conf")))
),
conditionalPanel(
condition = "input.culttest1_conf == input.culttest2_conf",
column(6, box(width = NULL, title = strong("Test sulla varianza"), status = "warning", tags$i(class = "fas fa-exclamation-triangle", style="font-size: 20px; color: rgb(243,156,18)"),
h5(strong("Errore. La variabile dipendente e il fattore esplicativo devono essere diversi.", style = "color: rgb(243,156,18)")), style = "text-align: justify; text-align: center;")),
column(6, box(width = NULL, title = strong("Test statistico"), status = "warning", tags$i(class = "fas fa-exclamation-triangle", style="font-size: 20px; color: rgb(243,156,18)"),
h5(strong("Errore. La variabile dipendente e il fattore esplicativo devono essere diversi.", style = "color: rgb(243,156,18)")), style = "text-align: justify; text-align: center;"))
),
conditionalPanel(
condition = "input.culttest1_conf != input.culttest2_conf && output.shapttestmorfoui_conf == 'distribuzione non normale' && input.selectttest_conf == 'T-test'",
column(6, offset = 3,
box(width = NULL, status = "warning", style = "text-align: justify; text-align: center;", br(),
tags$i(class = "fas fa-exclamation-triangle", style="font-size: 25px; color: rgb(243,156,18)"),
h4(strong("Una o più variabili non seguono una distribuzione normale. Scegli il Wilcoxon-Mann-Whitney test.", style = "color: rgb(243,156,18)")),
br()
)
)
)
),
fluidRow(
column(8, offset = 2, box(width = NULL, title = strong("Grafico"), status = "primary",
shinycssloaders::withSpinner(image = "www/running_olive.gif", plotly::plotlyOutput("boxttest_conf"))))
)
) #end of fluidpage
), #end of tabpanel conf 2 gruppi
# Confronto tra più gruppi
tabPanel(
"Confronto tra più gruppi", value = "tabpananova_conf",
fluidPage(
fluidRow(
column(12, box(width = NULL, title = strong("Boxplot"), status = "primary",
shinycssloaders::withSpinner(image = "www/running_olive.gif", plotly::plotlyOutput("boxanova_conf"))))
),
fluidRow(
column(6, box(width = NULL, title = strong("Test sulla normalità"), status = "primary", verbatimTextOutput("shapiroanova1_conf"))),
conditionalPanel(
condition = "(output.shapanovamorfoui_conf == 'distribuzione normale' && (input.selectanovatest2_conf == 'ANOVA' || input.selectanovatest2_conf == 'Kruskal-Wallis')) || (output.shapanovamorfoui_conf == 'distribuzione non normale' && input.selectanovatest2_conf == 'Kruskal-Wallis')",
conditionalPanel(condition = "input.selectanovatest2_conf == 'ANOVA'",
column(6, box(width = NULL, title = strong("Test ANOVA"), status = "primary", verbatimTextOutput("anova1morfoprint_conf")))
),
conditionalPanel(condition = "input.selectanovatest2_conf == 'Kruskal-Wallis'",
column(6, box(width = NULL, title = strong("Test Kruskal-Wallis"), status = "primary", verbatimTextOutput("kruskmorfo_conf")))
)
),
conditionalPanel(condition = "output.shapanovamorfoui_conf == 'distribuzione non normale' && input.selectanovatest2_conf == 'ANOVA'",
column(6, box(width = NULL, title = strong("Test ANOVA"), status = "warning", style = "text-align: justify; text-align: center;",
tags$i(class = "fas fa-exclamation-triangle", style="font-size: 25px; color: rgb(243,156,18)"),
h4(strong("La variabile numerica non segue la distribuzione normale. Scegli il test Kruskal-Wallis.", style = "color: rgb(243,156,18)")),
))
)
),
conditionalPanel(
condition = "(output.shapanovamorfoui_conf == 'distribuzione normale' && (input.selectanovatest2_conf == 'ANOVA' || input.selectanovatest2_conf == 'Kruskal-Wallis')) || (output.shapanovamorfoui_conf == 'distribuzione non normale' && input.selectanovatest2_conf == 'Kruskal-Wallis')",
fluidRow(
column(10,offset = 1,
box(width = NULL, title = strong("Post-hoc"), status = "primary", style = "text-align: justify; text-align: center;",
conditionalPanel(
condition = "output.signiftestmorfoui_conf == 'significativo'",
conditionalPanel(condition = "input.selectanovatest2_conf == 'ANOVA'",
h4(strong("Tukey HSD"))),
conditionalPanel(condition = "input.selectanovatest2_conf == 'Kruskal-Wallis'",
h4(strong("Dunn Test")),
),
shinycssloaders::withSpinner(image = "www/running_olive.gif", plotly::plotlyOutput("posthocmorfograph_conf"))
),
conditionalPanel(condition = "output.signiftestmorfoui_conf == 'non significativo'",
tags$i(class = "fas fa-exclamation-triangle", style="font-size: 25px; color: rgb(243,156,18)"),
h4(strong("Il p-value è maggiore del livello di significatività impostato. Non ci sono differenze significative tra le variabili.", style = "color: rgb(243,156,18)"))
)
)
)
) #end of fluidrow post-hoc
)
) #end of fluidpage
), #end of tabpanel più gruppi
#
#
#
#
# #Test d'indipendenza
# tabPanel("Test d'indipendenza", value = "tabpanchisqtestmorfo",
# br(),
# fluidPage(
# fluidRow(
# column(5, box(width = NULL, title = strong("Tabella di contingenza"), status = "primary", tableOutput("contingtablemorfo"))),
# column(6,
# fluidRow(
# box(width = NULL, title = strong("Test"), status = "primary", verbatimTextOutput("chisqmorfoprint"))
# ),
#
# fluidRow(
# conditionalPanel(condition = "output.signiftestchisqmorfoui == 'significativo'",
# #box(width = NULL, title = strong("Grafico residui"), status = "primary", style = "text-align: justify; text-align: center;",
# shinycssloaders::withSpinner(image = "www/running_olive.gif", plotOutput("plotresidchisq"))
# # )
#
# ),
# conditionalPanel(condition = "output.signiftestchisqmorfoui == 'non significativo'",
# box(width = NULL, status = "warning", style = "text-align: justify; text-align: center;",
# tags$i(class = "fas fa-exclamation-triangle", style="font-size: 25px; color: rgb(243,156,18)"),
# h4(strong("Il p-value è maggiore del livello di significatività impostato. Le variabili sono indipendenti.", style = "color: rgb(243,156,18)"))
# )
# )
# ) #end of fluidrow grafico
# )
# ) #end of first fluidrow
# )
# )
) #end of tabset panel
),
)# end tabbox integrazione
)
)
) #end tabitem integrazione
)#end of tabitems
)#end of dashboardbody
)#end of dashboardpage
)
)
) #end of taglist
}
#' Add external Resources to the Application
#'
#' This function is internally used to add external
#' resources inside the Shiny application.
#'
#' @import shiny
#' @importFrom golem add_resource_path activate_js favicon bundle_resources
#' @noRd
golem_add_external_resources <- function(){
add_resource_path(
'www', app_sys('app/www')
)
tags$head(
favicon(),
bundle_resources(
path = app_sys('app/www'),
app_title = 'OliveHealthR'
)
# Add here other external resources
# for example, you can add shinyalert::useShinyalert()
)
}
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