R/app_ui.R
In omorante/shinyepico: ShinyÉPICo
Defines functions
app_ui
# AVAILABLE METHODS
norm_options <- c(
"Raw",
"Illumina",
"Funnorm",
"Noob",
"SWAN",
"Quantile",
"Noob+Quantile"
)
hclust_methods <- c(
"single",
"complete",
"average",
"mcquitty",
"median",
"centroid"
)
`%dopar%` <- foreach::`%dopar%`
`%do%` <- foreach::`%do%`
`%>%` <- magrittr::`%>%`
#' The application User-Interface
#'
#' @param request Internal parameter for `{shiny}`.
#' DO NOT REMOVE.
#' @import shiny
#' @import shinyWidgets
#' @noRd
app_ui <- function(request) {
navbarPage(
title = div(
style = "padding: 1px 0px; width: '100%'",
img(
src = "images/logo_header.png",
width = 25,
height = 25
),
"shiny\u00C9PICo!"
),
windowTitle = HTML("shiny\u00C9PICo!</title><link rel='icon' type='image/gif/png' href='images/favicon.ico'>"),
id = "navbar_epic",
collapsible = TRUE,
theme = shinythemes::shinytheme("sandstone"),
tabPanel(
"Input",
titlePanel("Load iDATs and sample sheet"),
sidebarLayout(
sidebarPanel(
width = 3,
fileInput(
inputId = "fileinput_input",
"Upload Compressed Experiment Directory (zip)",
multiple = FALSE,
accept = c(
"application/zip",
"application/x-zip-compressed"
)
),
uiOutput("ui_button_input_load"),
h3(),
conditionalPanel(
"typeof output.samples_table != 'undefined'",
selectInput("select_input_samplenamevar", "",
choices =
c()
),
h3(),
selectInput("select_input_groupingvar", "", c()),
h3(),
selectInput("select_input_donorvar", "", c()),
h3(),
pickerInput(
inputId = "selected_samples",
label = "",
choices = c(),
options = list(
`actions-box` = TRUE,
size = 10,
`selected-text-format` = "count > 3"
),
multiple = TRUE
),
br(),
h5(strong("Custom Annotation:")),
switchInput(
inputId = "switch_input_customanno",
onLabel = "Yes",
offLabel = "No",
value = FALSE,
inline = FALSE
),
conditionalPanel(
condition = "input.switch_input_customanno == true",
pickerInput(
inputId = "select_input_customarray",
label = "Array|Annotation:",
choices = obtaining_annotations()
)),
h3(),
actionButton("button_input_next", "Continue")
)
),
mainPanel(
width = 9,
DT::DTOutput("samples_table") %>% shinycssloaders::withSpinner()
)
)
),
tabPanel(
"Normalization",
titlePanel("Normalization"),
sidebarLayout(
sidebarPanel(
width = 3,
selectInput("select_minfi_norm", "Select Normalization", norm_options),
div(
margin_left = "50px",
switchInput(
inputId = "select_minfi_dropcphs",
label = "Drop CpHs",
labelWidth = "fit",
value = TRUE,
inline = TRUE
),
switchInput(
inputId = "select_minfi_dropsnps",
label = "Drop SNPs",
labelWidth = "fit",
value = TRUE,
inline = TRUE
)
),
conditionalPanel(
"input.select_minfi_dropsnps",
sliderInput(
inputId = "slider_minfi_maf",
label = "Minimum MAF to filter",
min = 0,
max = 1,
step = 0.01,
value = 0,
width = "75%"
)
),
switchInput(
inputId = "select_minfi_chromosomes",
label = "Drop X/Y Chr.",
labelWidth = "fit",
value = FALSE
),
shinyjs::disabled(actionButton("button_minfi_select", "Select")),
h4(),
textOutput("text_minfi_probes")
),
mainPanel(
width = 9,
tabsetPanel(
tabPanel(
"Quality Control",
h4("Overall Signal"),
plotly::plotlyOutput("graph_minfi_qcraw") %>% shinycssloaders::withSpinner(),
h4("Bisulfite Conversion II"),
plotly::plotlyOutput("graph_minfi_bisulfiterawII") %>% shinycssloaders::withSpinner()
),
tabPanel(
"Density plot",
h4("Raw"),
plotly::plotlyOutput("graph_minfi_densityplotraw") %>% shinycssloaders::withSpinner(),
h4("Processed"),
plotly::plotlyOutput("graph_minfi_densityplot") %>% shinycssloaders::withSpinner()
),
tabPanel(
"Boxplot",
h4("Raw"),
plotOutput("graph_minfi_boxplotraw") %>% shinycssloaders::withSpinner(),
h4("Processed"),
plotOutput("graph_minfi_boxplot") %>% shinycssloaders::withSpinner()
),
tabPanel(
"SNPs Heatmap",
h4("SNPs beta-values (Raw)"),
plotly::plotlyOutput("graph_minfi_snps") %>% shinycssloaders::withSpinner()
),
tabPanel(
"Sex prediction",
h4("X vs Y chromosomes signal plot"),
plotly::plotlyOutput("graph_minfi_sex") %>% shinycssloaders::withSpinner(),
DT::DTOutput("table_minfi_sex") %>% shinycssloaders::withSpinner()
),
tabPanel(
"Principal Component Analysis",
h4("Processed"),
plotly::plotlyOutput("graph_minfi_pcaplot") %>% shinycssloaders::withSpinner(),
DT::DTOutput("table_minfi_pcaplot") %>% shinycssloaders::withSpinner(),
column(
6,
selectInput(
inputId = "select_minfi_pcaplot_pcx",
choices = c(),
label = "Select x variable"
),
selectInput(
inputId = "select_minfi_pcaplot_color",
choices = c(),
label = "Select color variable"
)
),
column(
6,
selectInput(
inputId = "select_minfi_pcaplot_pcy",
choices = c(),
label = "Select y variable"
)
),
actionButton("button_pca_update", "Update")
),
tabPanel(
"Correlations",
h4("Processed"),
plotly::plotlyOutput("graph_minfi_corrplot") %>% shinycssloaders::withSpinner(),
selectInput("select_minfi_typecorrplot", "Select data to plot", choices = c("p.value", "correlation value"), selected = "correlation value"),
DT::DTOutput("table_minfi_corrplot") %>% shinycssloaders::withSpinner()
)
)
)
)
),
tabPanel(
"DMPs",
titlePanel("Differentially Methylated Positions"),
sidebarLayout(
sidebarPanel(
width = 3,
h4("Linear Model Options"),
pickerInput(
inputId = "select_limma_voi",
label = "Select Variable of Interest",
choices = c(),
multiple = FALSE
),
pickerInput(
inputId = "checkbox_limma_covariables",
label = "Select linear model covariables",
choices = c(),
multiple = TRUE,
options = list(
`actions-box` = TRUE,
size = 10,
`selected-text-format` = "count > 3"
)
),
pickerInput(
inputId = "checkbox_limma_interactions",
label = "Select linear model interactions",
choices = c(),
multiple = TRUE,
options = list(
`actions-box` = TRUE,
size = 10,
`selected-text-format` = "count > 3"
)
),
switchInput(
inputId = "select_limma_weights",
label = "Array Weights",
labelWidth = "80px",
value = FALSE
),
shinyjs::disabled(
actionButton("button_limma_calculatemodel", "Generate Model")
),
tags$br(),
uiOutput("button_limma_calculatedifs_container")
),
mainPanel(
width = 9,
tabsetPanel(
id = "tabset_limma",
tabPanel(
"Model diagnosis",
value = "model_diagnosis",
h4("Sigma vs A plot"),
plotOutput("graph_limma_plotSA") %>% shinycssloaders::withSpinner(),
h4("Design matrix"),
DT::DTOutput("table_limma_design") %>% shinycssloaders::withSpinner()
),
tabPanel(
"Heatmap",
value = "differential_cpgs",
div(
style = "max-width:800px;margin:auto;",
fluidPage(
h4("Heatmap"),
textOutput("text_limma_heatmapcount"),
uiOutput("graph_limma_heatmapcontainer"),
h4("DMP counts in each contrast"),
tableOutput("table_limma_difcpgs") %>% shinycssloaders::withSpinner(),
fluidRow(
column(
6,
h4("Group options"),
selectizeInput(
"select_limma_groups2plot",
"Groups to plot",
c(),
multiple = TRUE,
options = list(plugins = list("remove_button", "drag_drop"))
),
selectizeInput(
"select_limma_contrasts2plot",
"Contrasts to plot",
c(),
multiple = TRUE,
options = list(plugins = list("remove_button", "drag_drop"))
),
h4("Data options"),
switchInput(
inputId = "select_limma_removebatch",
label = "Remove Batch Effect",
labelWidth = "100px",
value = FALSE,
disabled = TRUE
),
),
column(
6,
h4("Filtering options"),
sliderInput("slider_limma_deltab", "Min. DeltaBeta", 0, 1, 0.2),
sliderInput("slider_limma_adjpvalue", "Max. FDR", 0, 1, 0.05),
sliderInput("slider_limma_pvalue", "Max. p-value", 0, 1, 1)
)
),
h4("Clustering options",
align =
"left"
),
fluidRow(
column(
5,
selectInput(
"select_limma_clusteralg",
"Clustering algorithm",
c(
"single",
"complete",
"average",
"mcquitty",
"median",
"centroid"
),
"average"
),
selectInput(
"select_limma_clusterdist",
"Distance Function",
c("pearson", "spearman", "kendall", "euclidean"),
"pearson"
),
selectInput("select_limma_scale", "Scale", c("row", "none"), "row"),
tags$br()
),
column(
3,
offset = 1,
tags$br(),
switchInput(
inputId = "select_limma_graphstatic",
label = "Static Graph",
labelWidth = "100px",
value = TRUE
),
switchInput(
inputId = "select_limma_colv",
label = "Column Dendro.",
labelWidth = "100px",
value = TRUE
),
switchInput(
inputId = "select_limma_colsidecolors",
label = "Column Colors",
labelWidth = "100px",
value = FALSE
)
),
column(
3,
tags$br(),
switchInput(
inputId = "select_limma_rowsidecolors",
label = "Row Colors",
labelWidth = "100px",
value = FALSE
),
conditionalPanel(
"input.select_limma_rowsidecolors",
numericInput(
"select_limma_knumber",
"Clusters number",
value = 2,
min = 1,
max = Inf,
step = 1
)
),
shinyjs::disabled(actionButton("button_limma_heatmapcalc", "Update"))
)
)
)
)
),
tabPanel(
"DMPs Annotation",
h4("DMP Boxplot"),
plotOutput("graph_limma_indboxplot") %>% shinycssloaders::withSpinner(),
h4("DMPs Annotation"),
br(),
DT::DTOutput("table_limma_ann") %>% shinycssloaders::withSpinner(),
selectInput(inputId = "select_limma_anncontrast", label = "", choices = "", selected = ""),
actionButton(inputId = "button_limma_indboxplotcalc", label = "Plot")
)
)
)
)
),
tabPanel(
"DMRs",
titlePanel("Differentially Methylated Regions"),
sidebarLayout(
sidebarPanel(
width = 3,
pickerInput(
inputId = "select_dmrs_contrasts",
label = "Contrasts to calculate",
choices = c(),
options = list(
`actions-box` = TRUE,
size = 10,
`selected-text-format` = "count > 3"
),
multiple = TRUE
),
pickerInput(
inputId = "select_dmrs_regions",
label = "Type of DMRs",
choices = c("promoters", "genes", "CGI"),
selected = c("promoters", "genes", "CGI"),
options = list(
`actions-box` = TRUE,
size = 10,
`selected-text-format` = "count > 3"
),
multiple = TRUE
),
pickerInput(
inputId = "select_dmrs_platform",
label = "Array platform",
choices = c("450k", "EPIC"),
selected = c("EPIC"),
multiple = FALSE
),
sliderInput(
"slider_dmrs_cpgs",
label = "Min. CpGs in DMR",
min = 2,
max = 50,
value = 5
),
sliderInput(
"slider_dmrs_permutations",
label = "Number of permutations",
min = 1000,
max = 100000,
value = 50000
),
shinyjs::disabled(actionButton("button_dmrs_calculate", "Calculate"))
),
mainPanel(
width = 9,
tabsetPanel(
id = "tabset_dmrs",
tabPanel(
"Heatmap",
div(
style = "max-width:800px;margin:auto;",
fluidPage(
h4("DMRs Heatmap"),
textOutput("text_dmrs_heatmapcount"),
uiOutput("graph_dmrs_heatmapcontainer"),
h4("DMRs counts in each contrast"),
tableOutput("table_dmrs_count") %>% shinycssloaders::withSpinner(),
fluidRow(
column(
6,
h4("Group options"),
selectizeInput(
"select_dmrs_groups2plot",
"Groups to plot",
c(),
multiple = TRUE,
options = list(plugins = list("remove_button", "drag_drop"))
),
selectizeInput(
"select_dmrs_contrasts2plot",
"Contrasts to plot",
c(),
multiple = TRUE,
options = list(plugins = list("remove_button", "drag_drop"))
),
selectizeInput(
"select_dmrs_regions2plot",
"Regions to plot",
c(),
multiple = TRUE,
options = list(plugins = list("remove_button", "drag_drop"))
),
h4("Data options"),
switchInput(
inputId = "select_dmrs_removebatch",
label = "Remove Batch Effect",
labelWidth = "100px",
value = FALSE,
disabled = TRUE
),
),
column(
6,
h4("Filtering options"),
sliderInput("slider_dmrs_deltab", "Min. DeltaBeta", 0, 1, 0),
sliderInput("slider_dmrs_adjpvalue", "Max. FDR", 0, 1, 0.05),
sliderInput("slider_dmrs_pvalue", "Max. p-value", 0, 1, 1)
)
),
h4("Clustering options",
align =
"left"
),
fluidRow(
column(
5,
selectInput(
"select_dmrs_clusteralg",
"Clustering algorithm",
c(
"single",
"complete",
"average",
"mcquitty",
"median",
"centroid"
),
"average"
),
selectInput(
"select_dmrs_clusterdist",
"Distance Function",
c("pearson", "spearman", "kendall", "euclidean"),
"pearson"
),
selectInput("select_dmrs_scale", "Scale", c("row", "none"), "row"),
tags$br()
),
column(
3,
offset = 1,
tags$br(),
switchInput(
inputId = "select_dmrs_graphstatic",
label = "Static Graph",
labelWidth = "100px",
value = TRUE
),
switchInput(
inputId = "select_dmrs_colv",
label = "Column Dendro.",
labelWidth = "100px",
value = TRUE
),
switchInput(
inputId = "select_dmrs_colsidecolors",
label = "Column Colors",
labelWidth = "100px",
value = FALSE
)
),
column(
3,
tags$br(),
switchInput(
inputId = "select_dmrs_rowsidecolors",
label = "Row Colors",
labelWidth = "100px",
value = FALSE
),
conditionalPanel(
"input.select_dmrs_rowsidecolors",
numericInput(
"select_dmrs_knumber",
"Clusters number",
value = 2,
min = 1,
max = Inf,
step = 1
)
),
shinyjs::disabled(actionButton("button_dmrs_heatmapcalc", "Update"))
)
)
)
)
),
tabPanel(
"Single DMR plot",
h4("Genomic graph"),
plotOutput("graph_dmrs_singledmr") %>% shinycssloaders::withSpinner(),
# h4("GSEA graph"),
# plotOutput("graph_dmrs_singlegsea") %>% shinycssloaders::withSpinner(),
h4("DMRs table"),
div(
style = "display:inline-block",
selectInput(
"select_dmrs_selcont",
label = "Contrast",
choices = c()
)
),
div(
style = "display:inline-block",
selectInput("select_dmrs_selreg", label = "Region", choices = c())
),
DT::DTOutput("table_dmrs_table") %>% shinycssloaders::withSpinner(),
br(),
actionButton("button_dmrs_graphsingle", "Plot")
)
)
),
)
),
tabPanel(
"Export",
shinyjs::useShinyjs(),
h3("Download RObjects"),
pickerInput(
inputId = "select_export_objects2download",
label = "Selected objects",
choices = c("RGSet", "GenomicRatioSet", "fit", "design", "ebayestables", "Bvalues", "Mvalues", "global_difs", "dmr_results"),
selected = c("RGSet", "GenomicRatioSet", "fit", "design", "ebayestables", "Bvalues", "Mvalues", "global_difs"),
options = list(
`actions-box` = TRUE,
size = 10,
`selected-text-format` = "count > 3"
),
multiple = TRUE
),
downloadButton("download_export_robjects"),
p(
"Press to download the R objects used for the analysis (RGSet, GenomicRatioSet, Bvalues, Mvalues, etc.)"
),
h3("Download filtered bed files"),
fluidPage(
div(
style = "display:inline-block",
selectInput(
"select_export_analysistype",
"Analysis type",
c("DMPs", "DMRs"),
selected = "by contrast"
)
),
div(
style = "display:inline-block",
selectInput(
"select_export_bedtype",
"Subsetting mode",
c("by contrasts", "by heatmap cluster"),
selected = "by contrasts"
)
),
div(
style = "display:inline-block",
selectInput(
"select_export_genometype",
"Genome version",
c("hg19", "hg38"),
selected = "hg19"
)
),
),
downloadButton("download_export_filteredbeds"),
p(
"Press to download the created filtered lists of contrasts, or heatmap clusters,
with the chosen criteria, in BED format."
),
h3("Download Workflow Report"),
downloadButton("download_export_markdown"),
p(
"Press to download the report of all the steps follow and selected in the pipeline, and the results."
),
h3("Download Custom R Script"),
downloadButton("download_export_script"),
p(
"Press to download an R script with the main parameters and steps follow in the DMP/DMR pipeline, to reproduce the results later outside the shiny application."
),
h3("Download Heatmap"),
selectInput(
"select_export_heatmaptype",
label = "Heatmap type",
choices = c("DMPs", "DMRs"),
selected = "DMPs"
),
downloadButton("download_export_heatmaps"),
p("Press to download the custom heatmap in the gplots::heatmap.2 version.")
),
tabPanel(
"Help",
tabsetPanel(
tabPanel("Credits",
tags$head(tags$style(HTML(
"a {color: #0275d8}"
))),
img(
src = "images/logo.png",
width = 150
),
h1("shiny\u00C9PICo"),
h3(as.character(utils::packageVersion("shinyepico"))),
br(),
h4(
tags$a(href = "https://www.gnu.org/licenses/agpl-3.0.html", "GNU Affero GPLv3 License", target = "_blank")
),
h4("\u00A9 2020 Octavio Morante-Palacios"),
h4(
tags$a(href = "mailto:octaviompa@gmail.com?\u00C9PICo!", "octaviompa@gmail.com", target = "_blank")
),
p(
"shiny\u00C9PICo is a graphical interface based on Shiny. It is intended for importing and normalizing Illumina DNA methylation arrays (450k or EPIC), exploring DNA methylation data and also for following a statistical analysis to
detect differentially methylated CpGs and differentially methylated regions, and plotting them in useful and customable heatmaps."
),
p(
"For suggestions or bug reports, please use the",
tags$a(href = "https://github.com/omorante/shinyepico/issues", "GitHub", target = "_blank"),
"issues forum."
)
),
tabPanel("Manual",
tags$iframe(style="height:900px; scrolling=yes; border=0; width:100%", src="https://omorante.github.io/shinyepico/shiny_epico.pdf")
)
)
)
)
}
omorante/shinyepico documentation built on May 11, 2023, 7:21 p.m.
R Package Documentation
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Defines functions app_ui
# AVAILABLE METHODS
norm_options <- c(
"Raw",
"Illumina",
"Funnorm",
"Noob",
"SWAN",
"Quantile",
"Noob+Quantile"
)
hclust_methods <- c(
"single",
"complete",
"average",
"mcquitty",
"median",
"centroid"
)
`%dopar%` <- foreach::`%dopar%`
`%do%` <- foreach::`%do%`
`%>%` <- magrittr::`%>%`
#' The application User-Interface
#'
#' @param request Internal parameter for `{shiny}`.
#' DO NOT REMOVE.
#' @import shiny
#' @import shinyWidgets
#' @noRd
app_ui <- function(request) {
navbarPage(
title = div(
style = "padding: 1px 0px; width: '100%'",
img(
src = "images/logo_header.png",
width = 25,
height = 25
),
"shiny\u00C9PICo!"
),
windowTitle = HTML("shiny\u00C9PICo!</title><link rel='icon' type='image/gif/png' href='images/favicon.ico'>"),
id = "navbar_epic",
collapsible = TRUE,
theme = shinythemes::shinytheme("sandstone"),
tabPanel(
"Input",
titlePanel("Load iDATs and sample sheet"),
sidebarLayout(
sidebarPanel(
width = 3,
fileInput(
inputId = "fileinput_input",
"Upload Compressed Experiment Directory (zip)",
multiple = FALSE,
accept = c(
"application/zip",
"application/x-zip-compressed"
)
),
uiOutput("ui_button_input_load"),
h3(),
conditionalPanel(
"typeof output.samples_table != 'undefined'",
selectInput("select_input_samplenamevar", "",
choices =
c()
),
h3(),
selectInput("select_input_groupingvar", "", c()),
h3(),
selectInput("select_input_donorvar", "", c()),
h3(),
pickerInput(
inputId = "selected_samples",
label = "",
choices = c(),
options = list(
`actions-box` = TRUE,
size = 10,
`selected-text-format` = "count > 3"
),
multiple = TRUE
),
br(),
h5(strong("Custom Annotation:")),
switchInput(
inputId = "switch_input_customanno",
onLabel = "Yes",
offLabel = "No",
value = FALSE,
inline = FALSE
),
conditionalPanel(
condition = "input.switch_input_customanno == true",
pickerInput(
inputId = "select_input_customarray",
label = "Array|Annotation:",
choices = obtaining_annotations()
)),
h3(),
actionButton("button_input_next", "Continue")
)
),
mainPanel(
width = 9,
DT::DTOutput("samples_table") %>% shinycssloaders::withSpinner()
)
)
),
tabPanel(
"Normalization",
titlePanel("Normalization"),
sidebarLayout(
sidebarPanel(
width = 3,
selectInput("select_minfi_norm", "Select Normalization", norm_options),
div(
margin_left = "50px",
switchInput(
inputId = "select_minfi_dropcphs",
label = "Drop CpHs",
labelWidth = "fit",
value = TRUE,
inline = TRUE
),
switchInput(
inputId = "select_minfi_dropsnps",
label = "Drop SNPs",
labelWidth = "fit",
value = TRUE,
inline = TRUE
)
),
conditionalPanel(
"input.select_minfi_dropsnps",
sliderInput(
inputId = "slider_minfi_maf",
label = "Minimum MAF to filter",
min = 0,
max = 1,
step = 0.01,
value = 0,
width = "75%"
)
),
switchInput(
inputId = "select_minfi_chromosomes",
label = "Drop X/Y Chr.",
labelWidth = "fit",
value = FALSE
),
shinyjs::disabled(actionButton("button_minfi_select", "Select")),
h4(),
textOutput("text_minfi_probes")
),
mainPanel(
width = 9,
tabsetPanel(
tabPanel(
"Quality Control",
h4("Overall Signal"),
plotly::plotlyOutput("graph_minfi_qcraw") %>% shinycssloaders::withSpinner(),
h4("Bisulfite Conversion II"),
plotly::plotlyOutput("graph_minfi_bisulfiterawII") %>% shinycssloaders::withSpinner()
),
tabPanel(
"Density plot",
h4("Raw"),
plotly::plotlyOutput("graph_minfi_densityplotraw") %>% shinycssloaders::withSpinner(),
h4("Processed"),
plotly::plotlyOutput("graph_minfi_densityplot") %>% shinycssloaders::withSpinner()
),
tabPanel(
"Boxplot",
h4("Raw"),
plotOutput("graph_minfi_boxplotraw") %>% shinycssloaders::withSpinner(),
h4("Processed"),
plotOutput("graph_minfi_boxplot") %>% shinycssloaders::withSpinner()
),
tabPanel(
"SNPs Heatmap",
h4("SNPs beta-values (Raw)"),
plotly::plotlyOutput("graph_minfi_snps") %>% shinycssloaders::withSpinner()
),
tabPanel(
"Sex prediction",
h4("X vs Y chromosomes signal plot"),
plotly::plotlyOutput("graph_minfi_sex") %>% shinycssloaders::withSpinner(),
DT::DTOutput("table_minfi_sex") %>% shinycssloaders::withSpinner()
),
tabPanel(
"Principal Component Analysis",
h4("Processed"),
plotly::plotlyOutput("graph_minfi_pcaplot") %>% shinycssloaders::withSpinner(),
DT::DTOutput("table_minfi_pcaplot") %>% shinycssloaders::withSpinner(),
column(
6,
selectInput(
inputId = "select_minfi_pcaplot_pcx",
choices = c(),
label = "Select x variable"
),
selectInput(
inputId = "select_minfi_pcaplot_color",
choices = c(),
label = "Select color variable"
)
),
column(
6,
selectInput(
inputId = "select_minfi_pcaplot_pcy",
choices = c(),
label = "Select y variable"
)
),
actionButton("button_pca_update", "Update")
),
tabPanel(
"Correlations",
h4("Processed"),
plotly::plotlyOutput("graph_minfi_corrplot") %>% shinycssloaders::withSpinner(),
selectInput("select_minfi_typecorrplot", "Select data to plot", choices = c("p.value", "correlation value"), selected = "correlation value"),
DT::DTOutput("table_minfi_corrplot") %>% shinycssloaders::withSpinner()
)
)
)
)
),
tabPanel(
"DMPs",
titlePanel("Differentially Methylated Positions"),
sidebarLayout(
sidebarPanel(
width = 3,
h4("Linear Model Options"),
pickerInput(
inputId = "select_limma_voi",
label = "Select Variable of Interest",
choices = c(),
multiple = FALSE
),
pickerInput(
inputId = "checkbox_limma_covariables",
label = "Select linear model covariables",
choices = c(),
multiple = TRUE,
options = list(
`actions-box` = TRUE,
size = 10,
`selected-text-format` = "count > 3"
)
),
pickerInput(
inputId = "checkbox_limma_interactions",
label = "Select linear model interactions",
choices = c(),
multiple = TRUE,
options = list(
`actions-box` = TRUE,
size = 10,
`selected-text-format` = "count > 3"
)
),
switchInput(
inputId = "select_limma_weights",
label = "Array Weights",
labelWidth = "80px",
value = FALSE
),
shinyjs::disabled(
actionButton("button_limma_calculatemodel", "Generate Model")
),
tags$br(),
uiOutput("button_limma_calculatedifs_container")
),
mainPanel(
width = 9,
tabsetPanel(
id = "tabset_limma",
tabPanel(
"Model diagnosis",
value = "model_diagnosis",
h4("Sigma vs A plot"),
plotOutput("graph_limma_plotSA") %>% shinycssloaders::withSpinner(),
h4("Design matrix"),
DT::DTOutput("table_limma_design") %>% shinycssloaders::withSpinner()
),
tabPanel(
"Heatmap",
value = "differential_cpgs",
div(
style = "max-width:800px;margin:auto;",
fluidPage(
h4("Heatmap"),
textOutput("text_limma_heatmapcount"),
uiOutput("graph_limma_heatmapcontainer"),
h4("DMP counts in each contrast"),
tableOutput("table_limma_difcpgs") %>% shinycssloaders::withSpinner(),
fluidRow(
column(
6,
h4("Group options"),
selectizeInput(
"select_limma_groups2plot",
"Groups to plot",
c(),
multiple = TRUE,
options = list(plugins = list("remove_button", "drag_drop"))
),
selectizeInput(
"select_limma_contrasts2plot",
"Contrasts to plot",
c(),
multiple = TRUE,
options = list(plugins = list("remove_button", "drag_drop"))
),
h4("Data options"),
switchInput(
inputId = "select_limma_removebatch",
label = "Remove Batch Effect",
labelWidth = "100px",
value = FALSE,
disabled = TRUE
),
),
column(
6,
h4("Filtering options"),
sliderInput("slider_limma_deltab", "Min. DeltaBeta", 0, 1, 0.2),
sliderInput("slider_limma_adjpvalue", "Max. FDR", 0, 1, 0.05),
sliderInput("slider_limma_pvalue", "Max. p-value", 0, 1, 1)
)
),
h4("Clustering options",
align =
"left"
),
fluidRow(
column(
5,
selectInput(
"select_limma_clusteralg",
"Clustering algorithm",
c(
"single",
"complete",
"average",
"mcquitty",
"median",
"centroid"
),
"average"
),
selectInput(
"select_limma_clusterdist",
"Distance Function",
c("pearson", "spearman", "kendall", "euclidean"),
"pearson"
),
selectInput("select_limma_scale", "Scale", c("row", "none"), "row"),
tags$br()
),
column(
3,
offset = 1,
tags$br(),
switchInput(
inputId = "select_limma_graphstatic",
label = "Static Graph",
labelWidth = "100px",
value = TRUE
),
switchInput(
inputId = "select_limma_colv",
label = "Column Dendro.",
labelWidth = "100px",
value = TRUE
),
switchInput(
inputId = "select_limma_colsidecolors",
label = "Column Colors",
labelWidth = "100px",
value = FALSE
)
),
column(
3,
tags$br(),
switchInput(
inputId = "select_limma_rowsidecolors",
label = "Row Colors",
labelWidth = "100px",
value = FALSE
),
conditionalPanel(
"input.select_limma_rowsidecolors",
numericInput(
"select_limma_knumber",
"Clusters number",
value = 2,
min = 1,
max = Inf,
step = 1
)
),
shinyjs::disabled(actionButton("button_limma_heatmapcalc", "Update"))
)
)
)
)
),
tabPanel(
"DMPs Annotation",
h4("DMP Boxplot"),
plotOutput("graph_limma_indboxplot") %>% shinycssloaders::withSpinner(),
h4("DMPs Annotation"),
br(),
DT::DTOutput("table_limma_ann") %>% shinycssloaders::withSpinner(),
selectInput(inputId = "select_limma_anncontrast", label = "", choices = "", selected = ""),
actionButton(inputId = "button_limma_indboxplotcalc", label = "Plot")
)
)
)
)
),
tabPanel(
"DMRs",
titlePanel("Differentially Methylated Regions"),
sidebarLayout(
sidebarPanel(
width = 3,
pickerInput(
inputId = "select_dmrs_contrasts",
label = "Contrasts to calculate",
choices = c(),
options = list(
`actions-box` = TRUE,
size = 10,
`selected-text-format` = "count > 3"
),
multiple = TRUE
),
pickerInput(
inputId = "select_dmrs_regions",
label = "Type of DMRs",
choices = c("promoters", "genes", "CGI"),
selected = c("promoters", "genes", "CGI"),
options = list(
`actions-box` = TRUE,
size = 10,
`selected-text-format` = "count > 3"
),
multiple = TRUE
),
pickerInput(
inputId = "select_dmrs_platform",
label = "Array platform",
choices = c("450k", "EPIC"),
selected = c("EPIC"),
multiple = FALSE
),
sliderInput(
"slider_dmrs_cpgs",
label = "Min. CpGs in DMR",
min = 2,
max = 50,
value = 5
),
sliderInput(
"slider_dmrs_permutations",
label = "Number of permutations",
min = 1000,
max = 100000,
value = 50000
),
shinyjs::disabled(actionButton("button_dmrs_calculate", "Calculate"))
),
mainPanel(
width = 9,
tabsetPanel(
id = "tabset_dmrs",
tabPanel(
"Heatmap",
div(
style = "max-width:800px;margin:auto;",
fluidPage(
h4("DMRs Heatmap"),
textOutput("text_dmrs_heatmapcount"),
uiOutput("graph_dmrs_heatmapcontainer"),
h4("DMRs counts in each contrast"),
tableOutput("table_dmrs_count") %>% shinycssloaders::withSpinner(),
fluidRow(
column(
6,
h4("Group options"),
selectizeInput(
"select_dmrs_groups2plot",
"Groups to plot",
c(),
multiple = TRUE,
options = list(plugins = list("remove_button", "drag_drop"))
),
selectizeInput(
"select_dmrs_contrasts2plot",
"Contrasts to plot",
c(),
multiple = TRUE,
options = list(plugins = list("remove_button", "drag_drop"))
),
selectizeInput(
"select_dmrs_regions2plot",
"Regions to plot",
c(),
multiple = TRUE,
options = list(plugins = list("remove_button", "drag_drop"))
),
h4("Data options"),
switchInput(
inputId = "select_dmrs_removebatch",
label = "Remove Batch Effect",
labelWidth = "100px",
value = FALSE,
disabled = TRUE
),
),
column(
6,
h4("Filtering options"),
sliderInput("slider_dmrs_deltab", "Min. DeltaBeta", 0, 1, 0),
sliderInput("slider_dmrs_adjpvalue", "Max. FDR", 0, 1, 0.05),
sliderInput("slider_dmrs_pvalue", "Max. p-value", 0, 1, 1)
)
),
h4("Clustering options",
align =
"left"
),
fluidRow(
column(
5,
selectInput(
"select_dmrs_clusteralg",
"Clustering algorithm",
c(
"single",
"complete",
"average",
"mcquitty",
"median",
"centroid"
),
"average"
),
selectInput(
"select_dmrs_clusterdist",
"Distance Function",
c("pearson", "spearman", "kendall", "euclidean"),
"pearson"
),
selectInput("select_dmrs_scale", "Scale", c("row", "none"), "row"),
tags$br()
),
column(
3,
offset = 1,
tags$br(),
switchInput(
inputId = "select_dmrs_graphstatic",
label = "Static Graph",
labelWidth = "100px",
value = TRUE
),
switchInput(
inputId = "select_dmrs_colv",
label = "Column Dendro.",
labelWidth = "100px",
value = TRUE
),
switchInput(
inputId = "select_dmrs_colsidecolors",
label = "Column Colors",
labelWidth = "100px",
value = FALSE
)
),
column(
3,
tags$br(),
switchInput(
inputId = "select_dmrs_rowsidecolors",
label = "Row Colors",
labelWidth = "100px",
value = FALSE
),
conditionalPanel(
"input.select_dmrs_rowsidecolors",
numericInput(
"select_dmrs_knumber",
"Clusters number",
value = 2,
min = 1,
max = Inf,
step = 1
)
),
shinyjs::disabled(actionButton("button_dmrs_heatmapcalc", "Update"))
)
)
)
)
),
tabPanel(
"Single DMR plot",
h4("Genomic graph"),
plotOutput("graph_dmrs_singledmr") %>% shinycssloaders::withSpinner(),
# h4("GSEA graph"),
# plotOutput("graph_dmrs_singlegsea") %>% shinycssloaders::withSpinner(),
h4("DMRs table"),
div(
style = "display:inline-block",
selectInput(
"select_dmrs_selcont",
label = "Contrast",
choices = c()
)
),
div(
style = "display:inline-block",
selectInput("select_dmrs_selreg", label = "Region", choices = c())
),
DT::DTOutput("table_dmrs_table") %>% shinycssloaders::withSpinner(),
br(),
actionButton("button_dmrs_graphsingle", "Plot")
)
)
),
)
),
tabPanel(
"Export",
shinyjs::useShinyjs(),
h3("Download RObjects"),
pickerInput(
inputId = "select_export_objects2download",
label = "Selected objects",
choices = c("RGSet", "GenomicRatioSet", "fit", "design", "ebayestables", "Bvalues", "Mvalues", "global_difs", "dmr_results"),
selected = c("RGSet", "GenomicRatioSet", "fit", "design", "ebayestables", "Bvalues", "Mvalues", "global_difs"),
options = list(
`actions-box` = TRUE,
size = 10,
`selected-text-format` = "count > 3"
),
multiple = TRUE
),
downloadButton("download_export_robjects"),
p(
"Press to download the R objects used for the analysis (RGSet, GenomicRatioSet, Bvalues, Mvalues, etc.)"
),
h3("Download filtered bed files"),
fluidPage(
div(
style = "display:inline-block",
selectInput(
"select_export_analysistype",
"Analysis type",
c("DMPs", "DMRs"),
selected = "by contrast"
)
),
div(
style = "display:inline-block",
selectInput(
"select_export_bedtype",
"Subsetting mode",
c("by contrasts", "by heatmap cluster"),
selected = "by contrasts"
)
),
div(
style = "display:inline-block",
selectInput(
"select_export_genometype",
"Genome version",
c("hg19", "hg38"),
selected = "hg19"
)
),
),
downloadButton("download_export_filteredbeds"),
p(
"Press to download the created filtered lists of contrasts, or heatmap clusters,
with the chosen criteria, in BED format."
),
h3("Download Workflow Report"),
downloadButton("download_export_markdown"),
p(
"Press to download the report of all the steps follow and selected in the pipeline, and the results."
),
h3("Download Custom R Script"),
downloadButton("download_export_script"),
p(
"Press to download an R script with the main parameters and steps follow in the DMP/DMR pipeline, to reproduce the results later outside the shiny application."
),
h3("Download Heatmap"),
selectInput(
"select_export_heatmaptype",
label = "Heatmap type",
choices = c("DMPs", "DMRs"),
selected = "DMPs"
),
downloadButton("download_export_heatmaps"),
p("Press to download the custom heatmap in the gplots::heatmap.2 version.")
),
tabPanel(
"Help",
tabsetPanel(
tabPanel("Credits",
tags$head(tags$style(HTML(
"a {color: #0275d8}"
))),
img(
src = "images/logo.png",
width = 150
),
h1("shiny\u00C9PICo"),
h3(as.character(utils::packageVersion("shinyepico"))),
br(),
h4(
tags$a(href = "https://www.gnu.org/licenses/agpl-3.0.html", "GNU Affero GPLv3 License", target = "_blank")
),
h4("\u00A9 2020 Octavio Morante-Palacios"),
h4(
tags$a(href = "mailto:octaviompa@gmail.com?\u00C9PICo!", "octaviompa@gmail.com", target = "_blank")
),
p(
"shiny\u00C9PICo is a graphical interface based on Shiny. It is intended for importing and normalizing Illumina DNA methylation arrays (450k or EPIC), exploring DNA methylation data and also for following a statistical analysis to
detect differentially methylated CpGs and differentially methylated regions, and plotting them in useful and customable heatmaps."
),
p(
"For suggestions or bug reports, please use the",
tags$a(href = "https://github.com/omorante/shinyepico/issues", "GitHub", target = "_blank"),
"issues forum."
)
),
tabPanel("Manual",
tags$iframe(style="height:900px; scrolling=yes; border=0; width:100%", src="https://omorante.github.io/shinyepico/shiny_epico.pdf")
)
)
)
)
}
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