inst/phyloprofile/ui.R
In trvinh/test: PhyloProfile
#' Load packages
packages <- c("shiny", "shinyBS", "shinyjs", "DT", "devtools", "colourpicker")
source("R/functions.R")
install_packages(packages)
lapply(packages, library, character.only = TRUE)
if (!require("shinycssloaders")) {
devtools::install_github("andrewsali/shinycssloaders")
library(shinycssloaders)
}
#' Import function files
source_files = list.files(path = "R",
pattern = "*.R$",
full.names = TRUE)
lapply(source_files, source, .GlobalEnv)
#' MAIN UI ====================================================================
shinyUI(
fluidPage(
tags$style(type = "text/css", "body {padding-top: 80px;}"),
useShinyjs(),
# Application title
titlePanel("", windowTitle = "PhyloProfile"),
# TOP WELLPANEL FOR PLOT CONFIGURATION ---------------------------------
conditionalPanel(
condition = "input.tabs=='Main profile'",
wellPanel(
fluidRow(
column(
2,
radioButtons(
inputId = "x_axis",
label = "Choose type of x-axis:",
choices = list("taxa", "genes"),
selected = "taxa",
inline = TRUE
),
hr(),
checkboxInput(
"auto_update",
strong(em("Auto update plot")),
value = FALSE,
width = NULL
)
),
column(
1,
create_plot_size("width", "Width (px)", 600),
actionButton("main_plot_config", "Appearance")
),
column(
1,
create_plot_size("height", "Height (px)", 600)
),
column(
2,
uiOutput("var1_cutoff.ui")
),
column(
2,
uiOutput("var2_cutoff.ui")
),
column(
2,
uiOutput("percent_cutoff.ui")
),
column(
2,
numericInput(
"coortholog",
"Max co-orthologs",
min = 1,
max = 999,
step = 1,
value = 999,
width = 150
),
shinyBS::bsButton(
"reset_main",
"Reset cutoffs",
style = "danger",
icon = icon("backward")
)
)
)
)
),
conditionalPanel(
condition = "input.tabs=='Customized profile'",
wellPanel(
fluidRow(
column(
2,
radioButtons(
inputId = "x_axis_selected",
label = "Choose type of x-axis:",
choices = list("taxa", "genes"),
selected = "taxa",
inline = TRUE
),
hr(),
checkboxInput(
"auto_update_selected",
strong(em("Auto update plot")),
value = FALSE,
width = NULL
)
),
column(
1,
create_plot_size("selected_width", "Width (px)", 600),
actionButton("selected_plot_config", "Appearance")
),
column(
1,
create_plot_size("selected_height", "Height (px)", 600)
),
column(
2,
uiOutput("var1_filter.ui")
),
column(
2,
uiOutput("var2_filter.ui")
),
column(
2,
uiOutput("percent_filter.ui")
),
column(
2,
uiOutput("coortholog_filter.ui"),
shinyBS::bsButton(
"reset_selected",
"Reset cutoffs",
style = "danger",
icon = icon("backward")
)
)
)
)
),
# MAIN NARVARPAGE TABS -------------------------------------------------
navbarPage(
em(strong("PhyloProfile v1.0.0")),
id = "tabs",
collapsible = TRUE,
inverse = TRUE,
fluid = TRUE,
position = "fixed-top",
# INPUT TAB --------------------------------------------------------
tabPanel(
"Input & settings",
# * 1st column -------------------------------------------------
column(
4,
# ** Main input --------------------------------------------
strong(h4("Main input:")),
conditionalPanel(
condition = "input.do",
em(
strong("RELOAD THIS TOOL TO UPLOAD A NEW INPUT
FILE!!!",
style = "color:red")
)
),
selectInput(
"demo_data", label = h5("Use online demo data:"),
choices = list("None" = "none",
"AMPK-TOR" = "ampk-tor",
"LCA Microsporidia" = "lca-micros"),
selected = "none",
width = "80%"
),
uiOutput("no_internet_msg"),
uiOutput("demo_data_describe"),
uiOutput("main_input_file.ui"),
uiOutput("input_check.ui"),
fluidRow(
column(
6,
conditionalPanel(
condition = "output.check_oma_input",
shinyBS::bsButton("open_oma_windows",
"Get data from OMA"),
br()
)
)
),
# ** Variable 1 --------------------------------------------
fluidRow(
column(
4,
uiOutput("var1_id.ui")
),
column(
4,
selectInput(
"var1_aggregate_by",
label = h5("Aggregate by:"),
choices = list("Max" = "max",
"Min" = "min",
"Mean" = "mean",
"Median" = "median"),
selected = "max",
width = 130
)
),
column(
4,
selectInput(
"var1_relation", label = h5("Relationship:"),
choices = list("Prot-Prot" = "protein",
"Prot-Spec" = "species"),
selected = "protein",
width = 130
),
bsPopover(
"var1_relation",
"",
"select if variable is the comparison between
*seed protein - ortholog protein* or
*seed protein - search taxon*",
"top"
)
)
),
# ** Variable 2 --------------------------------------------
fluidRow(
column(
4,
uiOutput("var2_id.ui")
),
column(
4,
selectInput(
"var2_aggregate_by",
label = h5("Aggregate by:"),
choices = list("Max" = "max",
"Min" = "min",
"Mean" = "mean",
"Median" = "median"),
selected = "max",
width = 130
)
),
column(
4,
uiOutput("var2_relation.ui")
)
),
hr(),
# ** Domain input ------------------------------------------
strong(h4("Additional annotation input:")),
radioButtons(
inputId = "anno_location", label = "",
choices = list("from file", "from folder"),
selected = "from file",
inline = TRUE
),
uiOutput("domain_input_file.ui"),
hr(),
em(
a("Click here to download demo files",
href = "https://github.com/BIONF/phyloprofile-data",
target = "_blank")
)
),
# * 2nd column -------------------------------------------------
column(
3,
bsAlert("input_msg_ui"),
# ** List of new taxa --------------------------------------
conditionalPanel(
condition = "output.unk_taxa_status == 'unknown' ||
output.unk_taxa_status == 'ncbi' ||
output.unk_taxa_status == 'invalid'",
strong(h4("New taxa were found:")),
dataTableOutput("unk_taxa_full"),
br(),
downloadButton("unk_taxa.download", "Download ID list")
),
# ** Other input options -----------------------------------
conditionalPanel(
condition = "output.unk_taxa_status == 0",
strong(h4("Choose genes of interest:")),
radioButtons(
inputId = "gene_list_selected",
label = "",
choices = list("all", "from file"),
selected = "all",
inline = TRUE
),
conditionalPanel(
condition = "input.gene_list_selected
== 'from file'",
fileInput("list", "")
),
hr(),
checkboxInput(
"ordering",
strong("Order sequence IDs"),
value = TRUE
),
hr(),
HTML("<b>Order taxa</b>"),
radioButtons(
inputId = "order_taxa",
label = "",
choices = list("automatically",
"by user defined tree"),
selected = "automatically",
inline = TRUE
),
bsPopover("order_taxa", "",
"in newick format", "bottom"),
conditionalPanel(
condition = "input.order_taxa
== 'by user defined tree'",
fileInput("inputTree", "")
),
uiOutput("checkNewick.ui"),
hr(),
strong(h4("Other optional input:")),
shinyBS::bsButton("fasta_upload", "FASTA file(s)"),
h5(""),
shinyBS::bsButton("upload_gene_category",
"Gene categories"),
h5(""),
hr(),
strong(h4("Color configuration:")),
actionButton(
"set_color",
"Change colors",
style = "padding:4px; font-size:100%"
),
hr()
)
),
# * 3rd column -------------------------------------------------
column(
4,
# ** Msg for parsing new taxa ------------------------------
conditionalPanel(
condition = "output.unk_taxa_status == 'unknown' ||
output.unk_taxa_status == 'ncbi' ||
output.unk_taxa_status == 'invalid'",
conditionalPanel(
condition = "output.unk_taxa_status == 'invalid'",
HTML(
"<p><em>Some new taxa have
<span style=\"color: #ff0000;\">invalid IDs
</span> (either in newTaxa.txt or in the main
profile input or both). IDs of non-NCBI taxa
have to be greater than 2268208.</em></p>
<p><em>Please replace those IDs before
continuing!</em></p>"
)
),
conditionalPanel(
condition = "output.unk_taxa_status == 'unknown'",
HTML(
'<p><em>NCBI taxonomy information of some taxa
can neither</em></p><ul><li><em>be retrieved
from NCBI (<span style="color: #0000ff;
">Source="ncbi"</span>) nor </em></li>
<li><em>be found in
<span style="color: #ff0000;">
phyloprofile/data/newTaxa.txt</span> (<span
style="color: #0000ff;">Source="new"</span>)
file</em></li></ul><p><strong><em>Please add
taxonomy information for those unknown taxa and
<span style="color: #ff0000;"> reload the tool
</span> to continue!</em></strong></p>'
),
h5(""),
shinyBS::bsButton(
"add_taxa",
"Add taxonomy info",
disabled = FALSE,
style = "warning"
)
),
conditionalPanel(
condition = "output.unk_taxa_status == 'ncbi'",
HTML(
'<p><em>NCBI taxonomy information of some taxa
can either</em></p><ul><li><em>be retrieved
from NCBI (<span style="color: #0000ff;
">Source="ncbi"</span>) or </em></li>
<li><em>be found in
<span style="color: #ff0000;">
phyloprofile/data/newTaxa.txt</span> (<span
style="color: #0000ff;">Source="new"</span>)
file</em></li></ul><p><strong><em>Click here to
get required taxonomy information for those
taxa!</em></strong></p>'
),
h5(""),
shinyBS::bsButton(
"but_parse",
"Get taxonomy info",
disabled = FALSE,
style = "warning"
),
hr(),
uiOutput("end_parsing_msg"),
tableOutput("invalidID.output"),
hr(),
conditionalPanel(
condition = "output.unk_taxa_status
== 'invalid'",
downloadButton("invalidID.download",
"Download invalid IDs")
)
)
),
# ** List of ranks & available taxa ------------------------
conditionalPanel(
condition = "output.unk_taxa_status == 0",
strong(h4("Seed (super)taxon:")),
br(),
strong(h5("Select taxonomy rank:")),
withSpinner(
uiOutput("rank_select"),
proxy.height = "50px",
type = 7,
size = 0.5
),
br(),
strong(h5("Choose (super)taxon of interest:")),
withSpinner(
uiOutput("select"),
proxy.height = "50px",
type = 7,
size = 0.5
),
br(),
shinyBS::bsButton(
"do",
"PLOT",
type = "action",
style = "danger",
size = "large",
disabled = FALSE
),
h5("")
)
)
),
# MAIN PROFILE TAB =================================================
tabPanel(
"Main profile",
sidebarLayout(
# * sidebar panel for profile highlight --------------------
sidebarPanel(
uiOutput("total_gene_number.ui"),
column(
4,
numericInput(
"st_index",
"Show from:",
min = 1,
max = 1600,
value = 1,
width = 100
),
style = "padding:0px;"
),
column(
4,
numericInput(
"end_index",
"...to:",
min = 1,
max = 1600,
value = 30,
width = 100
),
style = "padding:0px;"
),
column(
4,
uiOutput("highlight_gene_ui")
),
bsPopover(
"highlight_gene_ui",
"",
"Select gene to highlight",
"bottom"
),
bsPopover(
"st_index",
"",
"Set start index for sequence range",
"bottom"
),
bsPopover(
"end_index",
"",
"Set end index for sequence range",
"bottom"
),
br(),
uiOutput("highlight_taxon_ui"),
checkboxInput(
"color_by_group",
strong("Highlight genes by categories"),
value = FALSE
),
conditionalPanel(
condition = "input.auto_update == false",
shinyBS::bsButton(
"update_btn",
"Update plot",
style = "warning",
icon("refresh")
)
)
),
# * main panel for profile plot ----------------------------
mainPanel(
conditionalPanel(
condition = "input.do > 0",
create_profile_plot_ui("main_profile")
)
# ,
# conditionalPanel(
# condition = "input.main_x_axis_guide == true |
# input.main_y_axis_guide == true",
# absolutePanel(
# id = "absAxis",
# bottom = 0, left = 0,
# heigh = NULL, width = NULL,
# fixed = TRUE,
# draggable = TRUE,
# style = "opacity: 0.80",
#
# uiOutput("mainAxisRender")
# )
# )
)
)
),
# CUSTOMIZED PROFILE TAB ===========================================
tabPanel(
"Customized profile",
sidebarLayout(
# * sidebar panel for subseting data -----------------------
sidebarPanel(
width = 4,
column(
12,
style = "padding:0px;",
strong("Select sequence(s) of interest:")
),
column(
12,
fluidRow(
column(
8,
style = "padding:0px;",
uiOutput("gene_in")
),
column(
4,
fileInput("custom_file", "", width = "100%")
)
)
),
column(
12,
style = "padding:0px;",
strong(
"Select (super)taxon/(super)taxa of interest:"
)
),
column(
12,
fluidRow(
column(
8,
style = "padding:0px;",
uiOutput("taxa_in")
),
column(
4,
h3(""),
shinyBS::bsButton("cus_taxa", "Browse...")
)
)
),
h5(""),
conditionalPanel(
condition = "input.auto_update == false",
shinyBS::bsButton(
"plot_custom",
"Update plot",
style = "warning",
icon("refresh")
)
)
),
# * main panel for customized profile plot -----------------
mainPanel(
conditionalPanel(
condition = "output.same_profile == true",
h4(
"Please select subset of genes and/
or taxa for customized profile!"
)
),
conditionalPanel(
condition = "input.do > 0",
create_profile_plot_ui("customized_profile")
)
)
)
),
# FUNCTION TAB =====================================================
navbarMenu(
"Function",
# * Profiles clustering ----------------------------------------
tabPanel(
"Profiles clustering",
h4(strong("Profiles clustering")),
bsAlert("desc_clustering_ui"),
wellPanel(
fluidRow(
column(
2,
uiOutput("select_profile_type")
),
column(
3,
uiOutput("select_dist_method")
),
column(
3,
selectInput(
"cluster_method",
label = h5("Cluster method:"),
choices = list(
"single" = "single",
"complete" = "complete",
"average (UPGMA)" = "average",
"mcquitty (WPGMA)" = "mcquitty",
"median (WPGMC)" = "median",
"centroid (UPGMC)" = "centroid"
),
selected = "complete"
)
),
column(
1,
create_plot_size(
"cluster_plot.width", "Width (px)", 600
)
),
column(
1,
create_plot_size(
"cluster_plot.height", "Height (px)", 600
)
),
column(
2,
checkboxInput(
"apply_cluster",
em(strong(
"Apply clustering to profile plot",
style = "color:darkblue"
)),
value = FALSE
),
uiOutput("apply_cluster_check.ui"),
checkboxInput(
"add_cluster_cutom_profile",
strong(em(
"Add selected genes to Customized
profile",
style = "color:red"
)),
value = FALSE,
width = NULL
),
uiOutput("add_cluster_cutom_profile_check.ui")
)
)
),
cluster_profile_ui("profile_clustering")
),
# * Distribution analysis --------------------------------------
tabPanel(
"Distribution analysis",
h4(strong("Distribution analysis")),
bsAlert("desc_distribution_ui"),
wellPanel(
fluidRow(
column(
2,
selectInput(
"dataset.distribution", "Select data",
choices = c("Main data", "Customized data"),
selected = "Main data"
),
uiOutput("selected.distribution")
),
column(
2,
uiOutput("var1_dist.ui")
),
column(
2,
uiOutput("var2_dist.ui")
),
column(
2,
uiOutput("percent_dist.ui")
),
column(
2,
create_text_size(
"dist_text_size", "Label size", 12, 100
)
),
column(
2,
create_plot_size(
"dist_width", "Width (px)", 600
)
)
)
),
analyze_distribution_ui("dist_plot")
),
# * Gene age estimation ----------------------------------------
tabPanel(
"Gene age estimation",
h4(strong("Gene age estimation")),
bsAlert("desc_gene_age_ui"),
wellPanel(
fluidRow(
column(
2,
uiOutput("var1_age.ui")
),
column(
2,
uiOutput("var2_age.ui")
),
column(
2,
uiOutput("percent_age.ui")
),
column(
2,
strong("Appearance"),
bsButton("gene_age_prot_config", "Plot config")
),
column(
4,
checkboxInput(
"add_gene_age_custom_profile",
strong(em(
"Add selected genes to Customized
profile",
style = "color:red"
)),
value = FALSE,
width = NULL
),
uiOutput("add_gene_age_custom_profile_check.ui")
)
)
),
plot_gene_age_ui("gene_age")
),
# * Core gene identification ----------------------------------
tabPanel(
"Core gene identification",
h4(strong("Core gene identification")),
bsAlert("desc_core_gene_ui"),
wellPanel(
fluidRow(
column(
3,
uiOutput("var1_core.ui")
),
column(
3,
uiOutput("var2_core.ui")
),
column(
3,
uiOutput("percent_core.ui")
),
column(
3,
sliderInput(
"core_coverage",
"Core taxa coverage",
min = 0,
max = 100,
value = 100,
step = 5
)
),
column(
12,
uiOutput("taxa_list_core.ui"),
shinyBS::bsButton("browse_taxa_core", "Browse")
)
)
),
hr(),
column(
4,
downloadButton("core_gene_table_download",
"Download gene list"),
checkboxInput(
"add_core_gene_custom_profile",
strong(em("Add core genes to Customized profile",
style = "color:red")),
value = FALSE,
width = NULL
),
uiOutput("add_core_gene_custom_profile_check.ui")
),
identify_core_gene_ui("core_gene")
),
# * Group Comparison ------------------------------------------
tabPanel(
"Group comparison",
h4(strong("Group comparison")),
bsAlert("desc_gc_ui"),
wellPanel(
fluidRow(
column(
3,
uiOutput("variable_button_gc"),
popify(
checkboxInput(
"right_format_features",
"Annotation format:
’Type_Name’",
value = TRUE,
width = NULL
),
"",
"E.g.: pfam_ApbA, smart_SRP54"
)
),
column(
2,
uiOutput("list_genes_gc"),
popify(
fileInput("gc_file", NULL, width = "100%"),
"",
"Upload list of genes of interest"
)
),
column(
2,
uiOutput("taxa_list_gc"), # Select In-Group
shinyBS::bsButton("taxa_gc", "Browse"),
checkboxInput(
"use_common_ancestor",
"Use common ancestor",
value = TRUE,
width = NULL
),
bsPopover(
"use_common_ancestor",
"",
"All taxa that have the same common ancestor
with the selected taxa above will be
considered as the in-group",
"top"
)
),
column(
3,
uiOutput("significance.ui"),
checkboxInput(
"add_gc_genes_custom_profile",
strong(em(
"Add candidate gene(s) to Customized
profile",
style = "color:red"
)),
value = FALSE,
width = NULL
),
uiOutput("add_gc_custom_profile_check")
),
column(
2,
popify(
actionButton("gc_plot_config",
"Plot config"),
"",
"Change the appearance of the plots"
),
hr(),
bsButton("plot_gc", "COMPARE!",
style = "warning")
)
)
),
group_comparison_ui("group_comparison")
),
# * Search for NCBI taxonomy IDs ------------------------------
search_taxon_id_ui("search_taxon_id")
),
# DATA DOWNLOAD TAB ================================================
navbarMenu(
"Download filtered data",
download_filtered_main_ui("filtered_main_download"),
download_filtered_customized_ui("filtered_customized_download")
),
# HELP TAB =========================================================
navbarMenu(
"Help",
tabPanel(
a(
"Wiki",
href = "https://github.com/BIONF/PhyloProfile/wiki",
target = "_blank"
)
),
tabPanel(
a(
"About",
href = "https://BIONF.github.io/PhyloProfile/",
target = "_blank"
)
)
)
),
# LIST OF POP-UP WINDOWS ===============================================
# * popup for getting taxa from OMA browser ----------------------------
bsModal(
"get_oma_data_windows",
"Get OMA data",
"open_oma_windows",
size = "small",
selectInput(
"selected_oma_type",
label = "Select type of OMA orthologs:",
choices = list("HOG", "OG"),# "PAIR"),
selected = "HOG"
),
shinyBS::bsButton("get_data_oma", "Get data", style = "danger"),
downloadButton("download_files_oma", "Save data"),
br(),
em("This windows will close automatically when eveything
is done!", style = "color:red")
),
# * popup for adding new taxa from input file --------------------------
bsModal(
"add_taxa_windows",
"Add new taxa",
"add_taxa",
size = "medium",
HTML(
"<p><em>Use this form to add taxon that does not exist in NCBI
taxonomy database (or alternatively you can manually prepare the
<span style=\"text-decoration: underline;\">
<span style=\"color: #ff0000; text-decoration: underline;\">
phyloprofile/data/newTaxa.txt file with the following
description for each field).</em></p>
<p><span style=\"color: #ff0000;\"><em><strong>
NOTE: ID and name of new taxon must be
<span style=\"text-decoration: underline;\">different</span>
from any existing NCBI taxa.</strong></em></span></p>"
),
textInput(
"new_id",
"ID (must be a number and greater than 2268208,
e.g. 9000001)",
9000001,
width = 500
),
textInput(
"new_name",
"Name (e.g. Saccharomyces cerevisiae strain ABC)",
"",
width = 500
),
textInput(
"new_rank",
"Rank (e.g. \"norank\" (for strain), species, order, etc.)",
"norank",
width = 500
),
textInput(
"new_parent",
"Parent ID (NCBI taxonomy ID of the next higher rank,
e.g. 4932 (S.cerevisiae species))",
4932,
width = 500
),
actionButton("new_add", "Add new taxon"),
hr(),
fileInput("new_taxa_file",
"Or upload file contains IDs for new taxa"),
HTML(
"<p><em>Taxonomy file for new taxa has to be a tab-delimited
text file and has the following header (please follow the rule
above):</em></p><p>ncbiID fullName rank
parentID</p>"
),
bsAlert("wrong_new_taxa"),
hr(),
shinyBS::bsButton("new_done", "Finish adding", style = "warning",
disabled = TRUE)
),
# * popup for confirming parsing taxa from input file ------------------
bsModal(
"parse_confirm",
"Get taxonomy info",
"but_parse",
size = "small",
HTML(
'<p>Fetching Missing Taxonomy Information and
Post-processing.</p><p><em>This windows will close
automatically when eveything is done. Please wait...</em></p>
<p><strong><span style="color: #ff0000;">PLEASE RELOAD THIS
TOOL WHEN FINISHED!!!</span></strong></p>'
)
),
# * popup for plotting detailed plot -----------------------------------
bsModal(
"modal_bs",
"Detailed plot",
"detailed_btn",
size = "large",
fluidRow(
column(
2,
create_plot_size("detailed_height", "Height (px)", 100)
),
column(
3,
create_text_size("detailed_text", "Text size (px)", 12, 150)
),
column(
7,
checkboxInput(
"detailed_remove_na",
strong("Hide taxa that have no ortholog (NAs)",
style = "color:red"),
value = FALSE
)
)
),
hr(),
create_detailed_plot_ui("detailed_plot"),
shinyBS::bsButton("do_domain_plot",
"Show domain architecture",
disabled = TRUE),
uiOutput("check_domain_files"),
br(),
h4("Sequence:"),
verbatimTextOutput("fasta")
),
# * popup for plotting domain architecture plot ------------------------
bsModal(
"plot_archi",
"Domain architecture",
"do_domain_plot",
size = "large",
fluidRow(
column(
2,
create_plot_size("archi_height", "Plot height(px)", 400)
),
column(
2,
create_plot_size("archi_width", "Plot width(px)", 800)
),
column(
2,
create_text_size("title_archi_size", "Title size(px)",
11, 150)
),
column(
2,
create_text_size("label_archi_size", "SeqID size(px)",
11, 150)
)
),
uiOutput("test.ui"),
create_architecture_plot_ui("archi_plot")
),
# * popup for setting plot colors (profiles) ---------------------------
bsModal(
"color",
"Set colors for profile",
"set_color",
size = "small",
colourpicker::colourInput(
"low_color_var1",
"Low variable 1 (dot)",
value = "darkorange"
),
colourpicker::colourInput(
"high_color_var1",
"High variable 1 (dot)",
value = "steelblue"
),
actionButton(
"default_color_var1",
"Default",
style = "padding:4px; font-size:100%"
),
hr(),
colourpicker::colourInput(
"low_color_var2",
"Low variable 2 (background)",
value = "grey95"
),
colourpicker::colourInput(
"high_color_var2",
"High variable 2 (background)",
value = "khaki"
),
actionButton(
"default_color_var2",
"Default",
style = "padding:4px; font-size:100%"
),
hr(),
colourpicker::colourInput(
"para_color",
"Color for inparalogs",
value = "#07d000"
),
actionButton(
"default_color_para",
"Default",
style = "padding:4px; font-size:100%"
)
),
# * popup for FASTA upload ---------------------------------------------
bsModal(
"fasta_upload_bs",
"FASTA upload",
"fasta_upload",
size = "small",
selectInput(
"input_type", "Choose location for:",
c("Concatenated fasta file", "Fasta folder")
),
hr(),
uiOutput("default_color_para.ui"),
conditionalPanel(
condition = "input.input_type == 'Concatenated fasta file'",
fileInput("concat_fasta", ""),
uiOutput("concat_fasta.exist_check")
),
conditionalPanel(
condition = "input.input_type == 'Fasta folder'",
textInput("path", "Main FULL path:", ""),
selectInput(
"dir_format", "Directory format:",
choices = list("path/speciesID.fa*" = 1,
"path/speciesID/speciesID.fa*" = 2),
selected = "Path/speciesID.fasta"
),
selectInput(
"file_ext", "File extension:",
choices = list("fa" = "fa",
"fasta" = "fasta",
"fas" = "fas",
"txt" = "txt"),
selected = "fa"
),
selectInput(
"id_format",
"ID format:",
choices = list(">speciesID:seqID" = 1,
">speciesID@seqID" = 2,
">speciesID|seqID" = 3,
">seqID" = 4),
selected = 4
)
)
),
# * popup for upload gene category -------------------------------------
bsModal(
"upload_gene_category_bs",
"Upload gene categories",
"upload_gene_category",
size = "small",
fileInput("gene_category", "")
),
# * popup for setting Main plot configurations -------------------------
bsModal(
"main_plot_config_bs",
"Plot appearance configuration",
"main_plot_config",
size = "small",
column(
6,
create_text_size("x_size", "X-axis label size (px)", 8, 100)
),
column(
6,
create_text_size("y_size", "Y-axis label size (px)", 8, 100)
),
column(
6,
create_text_size("legend_size", "Legend label size (px)",
8, 150)
),
column(
6,
selectInput(
"main_legend", label = "Legend position:",
choices = list("Right" = "right",
"Left" = "left",
"Top" = "top",
"Bottom" = "bottom",
"Hide" = "none"),
selected = "right",
width = 150
)
),
column(
12,
HTML("<strong>Angle for x-axis label</strong>:<br>"),
sliderInput(
"x_angle",
"",
min = 0,
max = 90,
step = 10,
value = 60,
width = 250
),
br()
),
column(
12,
HTML("<strong>Zooming factor (α) for dots on
profile</strong>:<br>"),
sliderInput(
"dot_zoom", "",
min = -1,
max = 3,
step = 0.1,
value = 0,
width = 250
),
HTML("<em>dot size = (1+α)*default_size<br>default_size
=[0:5]</em>"),
uiOutput("dot_size_info"),
br()
),
br(),
hr(),
shinyBS::bsButton("reset_main_config", "Reset", style = "danger"),
shinyBS::bsButton("applyMainConfig", "Done", style = "warning")
),
# * popup for setting Customized plot configurations -------------------
bsModal(
"selected_plot_config_bs",
"Plot appearance configuration",
"selected_plot_config",
size = "small",
column(
6,
create_text_size("x_size_select", "X-axis label size (px)",
8, 100)
),
column(
6,
create_text_size("y_size_select", "Y-axis label size (px)",
8, 100)
),
column(
6,
create_text_size("legend_size_select", "Legend label size (px)",
8, 150)
),
column(
6,
selectInput(
"selected_legend", label = "Legend position:",
choices = list("Right" = "right",
"Left" = "left",
"Top" = "top",
"Bottom" = "bottom",
"Hide" = "none"),
selected = "right",
width = 150
)
),
column(
12,
HTML("<strong>Angle for x-axis label</strong>:<br>"),
sliderInput(
"x_angle_select", "",
min = 0,
max = 90,
step = 10,
value = 60,
width = 250
),
br()
),
column(
12,
HTML("<strong>Zooming factor (α) for dots on
profile</strong>:<br>"),
sliderInput(
"dot_zoom_select", "",
min = -1,
max = 3,
step = 0.1,
value = 0,
width = 250
),
HTML("<em>dot size = (1+α)*default_size<br>
default_size=[0:5]</em>"),
uiOutput("dot_size_infoSelect"),
br()
),
br(),
hr(),
shinyBS::bsButton("reset_selected_config", "Reset",
style = "danger"),
shinyBS::bsButton("apply_selected_config", "Done",
style = "warning")
),
# * popup for setting Gene age plot configurations ---------------------
bsModal(
"gene_age_prot_config_bs",
"Plot appearance configuration",
"gene_age_prot_config",
size = "small",
sliderInput(
"gene_age_width",
"Width zoom (*600px)",
min = 0,
max = 5,
step = 0.1,
value = 1,
width = "100%"
),
sliderInput(
"gene_age_height", "Height zoom (*150px)",
min = 0,
max = 5,
step = 0.1,
value = 1,
width = "100%"
),
sliderInput(
"gene_age_text", "Text size zoom",
min = 0,
max = 5,
step = 0.1,
value = 1,
width = "100%"
),
br(),
hr(),
shinyBS::bsButton(
"reset_gene_age_prot_config",
"Reset",
style = "danger"
)
),
# * popup for setting Group compariosn plot configurations -------------
bsModal(
"gc_plot_config_bs",
"Plot appearance configuration",
"gc_plot_config",
size = "small",
column(
6,
create_text_size("x_size_gc", "X-axis label size (px)", 10, 100)
),
column(
6,
create_text_size("y_size_gc", "Y-axis label size (px)", 10, 100)
),
column(
6,
create_text_size("legend_size_gc", "Legend label size (px)",
10, 150)
),
column(
6,
selectInput(
"legend_gc", label = "Legend position:",
choices = list("Right" = "right",
"Left" = "left",
"Top" = "top",
"Bottom" = "bottom",
"Hide" = "none"),
selected = "right",
width = 150
)
),
column(
6,
create_text_size("p_values_size_gc", "P-value label size (px)",
10, 100)
),
column(
6,
selectInput(
"show_point_gc", label = "Show location parameter:",
choices = list("Mean" = "mean",
"Median" = "median"),
selected = "mean",
width = 150)
),
column(
12,
sliderInput(
"angle_gc", "Angle of the X-axis label",
min = 0,
max = 180,
step = 1,
value = 90,
width = 250
)
),
column(
12,
checkboxInput(
"show_p_value",
strong("Show P-Values"),
value = TRUE,
width = 250
)
),
column(
12,
popify(
checkboxInput(
"highlight_significant",
strong("Highlight significant plots"),
value = TRUE,
width = 250
),
"",
"If both variables are selected the significant plot
is colored"
)
),
br(),
hr(),
shinyBS::bsButton("reset_config_gc", "Reset", style = "danger"),
shinyBS::bsButton("apply_config_gc", "Done", style = "warning")
),
# * popup for select taxa on Customized Profile ------------------------
bsModal(
"cus_taxa_bs",
"Select taxon/taxa of interest",
"cus_taxa",
size = "small",
select_taxon_rank_ui("select_taxon_rank"),
checkboxInput(
"apply_cus_taxa",
strong("Apply to customized profile",
style = "color:red"),
value = FALSE
)
),
# * popup for select taxa on Core gene finding -------------------------
bsModal(
"browse_taxa_core_bs",
"Select taxon/taxa of interest",
"browse_taxa_core",
size = "small",
select_taxon_rank_ui("select_taxon_rank_core"),
checkboxInput(
"apply_core_taxa",
strong("Apply", style = "color:red"),
value = FALSE
)
),
# * popup for select taxa on Group comparison --------------------------
bsModal(
"taxa_gc_bs",
"Select taxon/taxa of interest",
"taxa_gc",
size = "small",
select_taxon_rank_ui("select_taxon_rank_gc"),
checkboxInput(
"apply_taxa_gc",
strong("Apply",
style = "color:red"),
value = FALSE
)
),
# POINT INFO BOX =======================================================
conditionalPanel(
condition =
"input.tabs=='Main profile' ||
input.tabs=='Customized profile'",
absolutePanel(
bottom = 5, left = 30,
fixed = TRUE,
draggable = TRUE,
h5("Point's info:"),
verbatimTextOutput("point_info"),
conditionalPanel(
condition = "output.point_info_status == 0",
shinyBS::bsButton(
"detailed_btn",
"Detailed plot",
style = "success",
disabled = FALSE
)
),
style = "opacity: 0.80"
)
)
)
)
trvinh/test documentation built on May 9, 2019, 2:26 a.m.
R Package Documentation
Browse R Packages
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
#' Load packages
packages <- c("shiny", "shinyBS", "shinyjs", "DT", "devtools", "colourpicker")
source("R/functions.R")
install_packages(packages)
lapply(packages, library, character.only = TRUE)
if (!require("shinycssloaders")) {
devtools::install_github("andrewsali/shinycssloaders")
library(shinycssloaders)
}
#' Import function files
source_files = list.files(path = "R",
pattern = "*.R$",
full.names = TRUE)
lapply(source_files, source, .GlobalEnv)
#' MAIN UI ====================================================================
shinyUI(
fluidPage(
tags$style(type = "text/css", "body {padding-top: 80px;}"),
useShinyjs(),
# Application title
titlePanel("", windowTitle = "PhyloProfile"),
# TOP WELLPANEL FOR PLOT CONFIGURATION ---------------------------------
conditionalPanel(
condition = "input.tabs=='Main profile'",
wellPanel(
fluidRow(
column(
2,
radioButtons(
inputId = "x_axis",
label = "Choose type of x-axis:",
choices = list("taxa", "genes"),
selected = "taxa",
inline = TRUE
),
hr(),
checkboxInput(
"auto_update",
strong(em("Auto update plot")),
value = FALSE,
width = NULL
)
),
column(
1,
create_plot_size("width", "Width (px)", 600),
actionButton("main_plot_config", "Appearance")
),
column(
1,
create_plot_size("height", "Height (px)", 600)
),
column(
2,
uiOutput("var1_cutoff.ui")
),
column(
2,
uiOutput("var2_cutoff.ui")
),
column(
2,
uiOutput("percent_cutoff.ui")
),
column(
2,
numericInput(
"coortholog",
"Max co-orthologs",
min = 1,
max = 999,
step = 1,
value = 999,
width = 150
),
shinyBS::bsButton(
"reset_main",
"Reset cutoffs",
style = "danger",
icon = icon("backward")
)
)
)
)
),
conditionalPanel(
condition = "input.tabs=='Customized profile'",
wellPanel(
fluidRow(
column(
2,
radioButtons(
inputId = "x_axis_selected",
label = "Choose type of x-axis:",
choices = list("taxa", "genes"),
selected = "taxa",
inline = TRUE
),
hr(),
checkboxInput(
"auto_update_selected",
strong(em("Auto update plot")),
value = FALSE,
width = NULL
)
),
column(
1,
create_plot_size("selected_width", "Width (px)", 600),
actionButton("selected_plot_config", "Appearance")
),
column(
1,
create_plot_size("selected_height", "Height (px)", 600)
),
column(
2,
uiOutput("var1_filter.ui")
),
column(
2,
uiOutput("var2_filter.ui")
),
column(
2,
uiOutput("percent_filter.ui")
),
column(
2,
uiOutput("coortholog_filter.ui"),
shinyBS::bsButton(
"reset_selected",
"Reset cutoffs",
style = "danger",
icon = icon("backward")
)
)
)
)
),
# MAIN NARVARPAGE TABS -------------------------------------------------
navbarPage(
em(strong("PhyloProfile v1.0.0")),
id = "tabs",
collapsible = TRUE,
inverse = TRUE,
fluid = TRUE,
position = "fixed-top",
# INPUT TAB --------------------------------------------------------
tabPanel(
"Input & settings",
# * 1st column -------------------------------------------------
column(
4,
# ** Main input --------------------------------------------
strong(h4("Main input:")),
conditionalPanel(
condition = "input.do",
em(
strong("RELOAD THIS TOOL TO UPLOAD A NEW INPUT
FILE!!!",
style = "color:red")
)
),
selectInput(
"demo_data", label = h5("Use online demo data:"),
choices = list("None" = "none",
"AMPK-TOR" = "ampk-tor",
"LCA Microsporidia" = "lca-micros"),
selected = "none",
width = "80%"
),
uiOutput("no_internet_msg"),
uiOutput("demo_data_describe"),
uiOutput("main_input_file.ui"),
uiOutput("input_check.ui"),
fluidRow(
column(
6,
conditionalPanel(
condition = "output.check_oma_input",
shinyBS::bsButton("open_oma_windows",
"Get data from OMA"),
br()
)
)
),
# ** Variable 1 --------------------------------------------
fluidRow(
column(
4,
uiOutput("var1_id.ui")
),
column(
4,
selectInput(
"var1_aggregate_by",
label = h5("Aggregate by:"),
choices = list("Max" = "max",
"Min" = "min",
"Mean" = "mean",
"Median" = "median"),
selected = "max",
width = 130
)
),
column(
4,
selectInput(
"var1_relation", label = h5("Relationship:"),
choices = list("Prot-Prot" = "protein",
"Prot-Spec" = "species"),
selected = "protein",
width = 130
),
bsPopover(
"var1_relation",
"",
"select if variable is the comparison between
*seed protein - ortholog protein* or
*seed protein - search taxon*",
"top"
)
)
),
# ** Variable 2 --------------------------------------------
fluidRow(
column(
4,
uiOutput("var2_id.ui")
),
column(
4,
selectInput(
"var2_aggregate_by",
label = h5("Aggregate by:"),
choices = list("Max" = "max",
"Min" = "min",
"Mean" = "mean",
"Median" = "median"),
selected = "max",
width = 130
)
),
column(
4,
uiOutput("var2_relation.ui")
)
),
hr(),
# ** Domain input ------------------------------------------
strong(h4("Additional annotation input:")),
radioButtons(
inputId = "anno_location", label = "",
choices = list("from file", "from folder"),
selected = "from file",
inline = TRUE
),
uiOutput("domain_input_file.ui"),
hr(),
em(
a("Click here to download demo files",
href = "https://github.com/BIONF/phyloprofile-data",
target = "_blank")
)
),
# * 2nd column -------------------------------------------------
column(
3,
bsAlert("input_msg_ui"),
# ** List of new taxa --------------------------------------
conditionalPanel(
condition = "output.unk_taxa_status == 'unknown' ||
output.unk_taxa_status == 'ncbi' ||
output.unk_taxa_status == 'invalid'",
strong(h4("New taxa were found:")),
dataTableOutput("unk_taxa_full"),
br(),
downloadButton("unk_taxa.download", "Download ID list")
),
# ** Other input options -----------------------------------
conditionalPanel(
condition = "output.unk_taxa_status == 0",
strong(h4("Choose genes of interest:")),
radioButtons(
inputId = "gene_list_selected",
label = "",
choices = list("all", "from file"),
selected = "all",
inline = TRUE
),
conditionalPanel(
condition = "input.gene_list_selected
== 'from file'",
fileInput("list", "")
),
hr(),
checkboxInput(
"ordering",
strong("Order sequence IDs"),
value = TRUE
),
hr(),
HTML("<b>Order taxa</b>"),
radioButtons(
inputId = "order_taxa",
label = "",
choices = list("automatically",
"by user defined tree"),
selected = "automatically",
inline = TRUE
),
bsPopover("order_taxa", "",
"in newick format", "bottom"),
conditionalPanel(
condition = "input.order_taxa
== 'by user defined tree'",
fileInput("inputTree", "")
),
uiOutput("checkNewick.ui"),
hr(),
strong(h4("Other optional input:")),
shinyBS::bsButton("fasta_upload", "FASTA file(s)"),
h5(""),
shinyBS::bsButton("upload_gene_category",
"Gene categories"),
h5(""),
hr(),
strong(h4("Color configuration:")),
actionButton(
"set_color",
"Change colors",
style = "padding:4px; font-size:100%"
),
hr()
)
),
# * 3rd column -------------------------------------------------
column(
4,
# ** Msg for parsing new taxa ------------------------------
conditionalPanel(
condition = "output.unk_taxa_status == 'unknown' ||
output.unk_taxa_status == 'ncbi' ||
output.unk_taxa_status == 'invalid'",
conditionalPanel(
condition = "output.unk_taxa_status == 'invalid'",
HTML(
"<p><em>Some new taxa have
<span style=\"color: #ff0000;\">invalid IDs
</span> (either in newTaxa.txt or in the main
profile input or both). IDs of non-NCBI taxa
have to be greater than 2268208.</em></p>
<p><em>Please replace those IDs before
continuing!</em></p>"
)
),
conditionalPanel(
condition = "output.unk_taxa_status == 'unknown'",
HTML(
'<p><em>NCBI taxonomy information of some taxa
can neither</em></p><ul><li><em>be retrieved
from NCBI (<span style="color: #0000ff;
">Source="ncbi"</span>) nor </em></li>
<li><em>be found in
<span style="color: #ff0000;">
phyloprofile/data/newTaxa.txt</span> (<span
style="color: #0000ff;">Source="new"</span>)
file</em></li></ul><p><strong><em>Please add
taxonomy information for those unknown taxa and
<span style="color: #ff0000;"> reload the tool
</span> to continue!</em></strong></p>'
),
h5(""),
shinyBS::bsButton(
"add_taxa",
"Add taxonomy info",
disabled = FALSE,
style = "warning"
)
),
conditionalPanel(
condition = "output.unk_taxa_status == 'ncbi'",
HTML(
'<p><em>NCBI taxonomy information of some taxa
can either</em></p><ul><li><em>be retrieved
from NCBI (<span style="color: #0000ff;
">Source="ncbi"</span>) or </em></li>
<li><em>be found in
<span style="color: #ff0000;">
phyloprofile/data/newTaxa.txt</span> (<span
style="color: #0000ff;">Source="new"</span>)
file</em></li></ul><p><strong><em>Click here to
get required taxonomy information for those
taxa!</em></strong></p>'
),
h5(""),
shinyBS::bsButton(
"but_parse",
"Get taxonomy info",
disabled = FALSE,
style = "warning"
),
hr(),
uiOutput("end_parsing_msg"),
tableOutput("invalidID.output"),
hr(),
conditionalPanel(
condition = "output.unk_taxa_status
== 'invalid'",
downloadButton("invalidID.download",
"Download invalid IDs")
)
)
),
# ** List of ranks & available taxa ------------------------
conditionalPanel(
condition = "output.unk_taxa_status == 0",
strong(h4("Seed (super)taxon:")),
br(),
strong(h5("Select taxonomy rank:")),
withSpinner(
uiOutput("rank_select"),
proxy.height = "50px",
type = 7,
size = 0.5
),
br(),
strong(h5("Choose (super)taxon of interest:")),
withSpinner(
uiOutput("select"),
proxy.height = "50px",
type = 7,
size = 0.5
),
br(),
shinyBS::bsButton(
"do",
"PLOT",
type = "action",
style = "danger",
size = "large",
disabled = FALSE
),
h5("")
)
)
),
# MAIN PROFILE TAB =================================================
tabPanel(
"Main profile",
sidebarLayout(
# * sidebar panel for profile highlight --------------------
sidebarPanel(
uiOutput("total_gene_number.ui"),
column(
4,
numericInput(
"st_index",
"Show from:",
min = 1,
max = 1600,
value = 1,
width = 100
),
style = "padding:0px;"
),
column(
4,
numericInput(
"end_index",
"...to:",
min = 1,
max = 1600,
value = 30,
width = 100
),
style = "padding:0px;"
),
column(
4,
uiOutput("highlight_gene_ui")
),
bsPopover(
"highlight_gene_ui",
"",
"Select gene to highlight",
"bottom"
),
bsPopover(
"st_index",
"",
"Set start index for sequence range",
"bottom"
),
bsPopover(
"end_index",
"",
"Set end index for sequence range",
"bottom"
),
br(),
uiOutput("highlight_taxon_ui"),
checkboxInput(
"color_by_group",
strong("Highlight genes by categories"),
value = FALSE
),
conditionalPanel(
condition = "input.auto_update == false",
shinyBS::bsButton(
"update_btn",
"Update plot",
style = "warning",
icon("refresh")
)
)
),
# * main panel for profile plot ----------------------------
mainPanel(
conditionalPanel(
condition = "input.do > 0",
create_profile_plot_ui("main_profile")
)
# ,
# conditionalPanel(
# condition = "input.main_x_axis_guide == true |
# input.main_y_axis_guide == true",
# absolutePanel(
# id = "absAxis",
# bottom = 0, left = 0,
# heigh = NULL, width = NULL,
# fixed = TRUE,
# draggable = TRUE,
# style = "opacity: 0.80",
#
# uiOutput("mainAxisRender")
# )
# )
)
)
),
# CUSTOMIZED PROFILE TAB ===========================================
tabPanel(
"Customized profile",
sidebarLayout(
# * sidebar panel for subseting data -----------------------
sidebarPanel(
width = 4,
column(
12,
style = "padding:0px;",
strong("Select sequence(s) of interest:")
),
column(
12,
fluidRow(
column(
8,
style = "padding:0px;",
uiOutput("gene_in")
),
column(
4,
fileInput("custom_file", "", width = "100%")
)
)
),
column(
12,
style = "padding:0px;",
strong(
"Select (super)taxon/(super)taxa of interest:"
)
),
column(
12,
fluidRow(
column(
8,
style = "padding:0px;",
uiOutput("taxa_in")
),
column(
4,
h3(""),
shinyBS::bsButton("cus_taxa", "Browse...")
)
)
),
h5(""),
conditionalPanel(
condition = "input.auto_update == false",
shinyBS::bsButton(
"plot_custom",
"Update plot",
style = "warning",
icon("refresh")
)
)
),
# * main panel for customized profile plot -----------------
mainPanel(
conditionalPanel(
condition = "output.same_profile == true",
h4(
"Please select subset of genes and/
or taxa for customized profile!"
)
),
conditionalPanel(
condition = "input.do > 0",
create_profile_plot_ui("customized_profile")
)
)
)
),
# FUNCTION TAB =====================================================
navbarMenu(
"Function",
# * Profiles clustering ----------------------------------------
tabPanel(
"Profiles clustering",
h4(strong("Profiles clustering")),
bsAlert("desc_clustering_ui"),
wellPanel(
fluidRow(
column(
2,
uiOutput("select_profile_type")
),
column(
3,
uiOutput("select_dist_method")
),
column(
3,
selectInput(
"cluster_method",
label = h5("Cluster method:"),
choices = list(
"single" = "single",
"complete" = "complete",
"average (UPGMA)" = "average",
"mcquitty (WPGMA)" = "mcquitty",
"median (WPGMC)" = "median",
"centroid (UPGMC)" = "centroid"
),
selected = "complete"
)
),
column(
1,
create_plot_size(
"cluster_plot.width", "Width (px)", 600
)
),
column(
1,
create_plot_size(
"cluster_plot.height", "Height (px)", 600
)
),
column(
2,
checkboxInput(
"apply_cluster",
em(strong(
"Apply clustering to profile plot",
style = "color:darkblue"
)),
value = FALSE
),
uiOutput("apply_cluster_check.ui"),
checkboxInput(
"add_cluster_cutom_profile",
strong(em(
"Add selected genes to Customized
profile",
style = "color:red"
)),
value = FALSE,
width = NULL
),
uiOutput("add_cluster_cutom_profile_check.ui")
)
)
),
cluster_profile_ui("profile_clustering")
),
# * Distribution analysis --------------------------------------
tabPanel(
"Distribution analysis",
h4(strong("Distribution analysis")),
bsAlert("desc_distribution_ui"),
wellPanel(
fluidRow(
column(
2,
selectInput(
"dataset.distribution", "Select data",
choices = c("Main data", "Customized data"),
selected = "Main data"
),
uiOutput("selected.distribution")
),
column(
2,
uiOutput("var1_dist.ui")
),
column(
2,
uiOutput("var2_dist.ui")
),
column(
2,
uiOutput("percent_dist.ui")
),
column(
2,
create_text_size(
"dist_text_size", "Label size", 12, 100
)
),
column(
2,
create_plot_size(
"dist_width", "Width (px)", 600
)
)
)
),
analyze_distribution_ui("dist_plot")
),
# * Gene age estimation ----------------------------------------
tabPanel(
"Gene age estimation",
h4(strong("Gene age estimation")),
bsAlert("desc_gene_age_ui"),
wellPanel(
fluidRow(
column(
2,
uiOutput("var1_age.ui")
),
column(
2,
uiOutput("var2_age.ui")
),
column(
2,
uiOutput("percent_age.ui")
),
column(
2,
strong("Appearance"),
bsButton("gene_age_prot_config", "Plot config")
),
column(
4,
checkboxInput(
"add_gene_age_custom_profile",
strong(em(
"Add selected genes to Customized
profile",
style = "color:red"
)),
value = FALSE,
width = NULL
),
uiOutput("add_gene_age_custom_profile_check.ui")
)
)
),
plot_gene_age_ui("gene_age")
),
# * Core gene identification ----------------------------------
tabPanel(
"Core gene identification",
h4(strong("Core gene identification")),
bsAlert("desc_core_gene_ui"),
wellPanel(
fluidRow(
column(
3,
uiOutput("var1_core.ui")
),
column(
3,
uiOutput("var2_core.ui")
),
column(
3,
uiOutput("percent_core.ui")
),
column(
3,
sliderInput(
"core_coverage",
"Core taxa coverage",
min = 0,
max = 100,
value = 100,
step = 5
)
),
column(
12,
uiOutput("taxa_list_core.ui"),
shinyBS::bsButton("browse_taxa_core", "Browse")
)
)
),
hr(),
column(
4,
downloadButton("core_gene_table_download",
"Download gene list"),
checkboxInput(
"add_core_gene_custom_profile",
strong(em("Add core genes to Customized profile",
style = "color:red")),
value = FALSE,
width = NULL
),
uiOutput("add_core_gene_custom_profile_check.ui")
),
identify_core_gene_ui("core_gene")
),
# * Group Comparison ------------------------------------------
tabPanel(
"Group comparison",
h4(strong("Group comparison")),
bsAlert("desc_gc_ui"),
wellPanel(
fluidRow(
column(
3,
uiOutput("variable_button_gc"),
popify(
checkboxInput(
"right_format_features",
"Annotation format:
’Type_Name’",
value = TRUE,
width = NULL
),
"",
"E.g.: pfam_ApbA, smart_SRP54"
)
),
column(
2,
uiOutput("list_genes_gc"),
popify(
fileInput("gc_file", NULL, width = "100%"),
"",
"Upload list of genes of interest"
)
),
column(
2,
uiOutput("taxa_list_gc"), # Select In-Group
shinyBS::bsButton("taxa_gc", "Browse"),
checkboxInput(
"use_common_ancestor",
"Use common ancestor",
value = TRUE,
width = NULL
),
bsPopover(
"use_common_ancestor",
"",
"All taxa that have the same common ancestor
with the selected taxa above will be
considered as the in-group",
"top"
)
),
column(
3,
uiOutput("significance.ui"),
checkboxInput(
"add_gc_genes_custom_profile",
strong(em(
"Add candidate gene(s) to Customized
profile",
style = "color:red"
)),
value = FALSE,
width = NULL
),
uiOutput("add_gc_custom_profile_check")
),
column(
2,
popify(
actionButton("gc_plot_config",
"Plot config"),
"",
"Change the appearance of the plots"
),
hr(),
bsButton("plot_gc", "COMPARE!",
style = "warning")
)
)
),
group_comparison_ui("group_comparison")
),
# * Search for NCBI taxonomy IDs ------------------------------
search_taxon_id_ui("search_taxon_id")
),
# DATA DOWNLOAD TAB ================================================
navbarMenu(
"Download filtered data",
download_filtered_main_ui("filtered_main_download"),
download_filtered_customized_ui("filtered_customized_download")
),
# HELP TAB =========================================================
navbarMenu(
"Help",
tabPanel(
a(
"Wiki",
href = "https://github.com/BIONF/PhyloProfile/wiki",
target = "_blank"
)
),
tabPanel(
a(
"About",
href = "https://BIONF.github.io/PhyloProfile/",
target = "_blank"
)
)
)
),
# LIST OF POP-UP WINDOWS ===============================================
# * popup for getting taxa from OMA browser ----------------------------
bsModal(
"get_oma_data_windows",
"Get OMA data",
"open_oma_windows",
size = "small",
selectInput(
"selected_oma_type",
label = "Select type of OMA orthologs:",
choices = list("HOG", "OG"),# "PAIR"),
selected = "HOG"
),
shinyBS::bsButton("get_data_oma", "Get data", style = "danger"),
downloadButton("download_files_oma", "Save data"),
br(),
em("This windows will close automatically when eveything
is done!", style = "color:red")
),
# * popup for adding new taxa from input file --------------------------
bsModal(
"add_taxa_windows",
"Add new taxa",
"add_taxa",
size = "medium",
HTML(
"<p><em>Use this form to add taxon that does not exist in NCBI
taxonomy database (or alternatively you can manually prepare the
<span style=\"text-decoration: underline;\">
<span style=\"color: #ff0000; text-decoration: underline;\">
phyloprofile/data/newTaxa.txt file with the following
description for each field).</em></p>
<p><span style=\"color: #ff0000;\"><em><strong>
NOTE: ID and name of new taxon must be
<span style=\"text-decoration: underline;\">different</span>
from any existing NCBI taxa.</strong></em></span></p>"
),
textInput(
"new_id",
"ID (must be a number and greater than 2268208,
e.g. 9000001)",
9000001,
width = 500
),
textInput(
"new_name",
"Name (e.g. Saccharomyces cerevisiae strain ABC)",
"",
width = 500
),
textInput(
"new_rank",
"Rank (e.g. \"norank\" (for strain), species, order, etc.)",
"norank",
width = 500
),
textInput(
"new_parent",
"Parent ID (NCBI taxonomy ID of the next higher rank,
e.g. 4932 (S.cerevisiae species))",
4932,
width = 500
),
actionButton("new_add", "Add new taxon"),
hr(),
fileInput("new_taxa_file",
"Or upload file contains IDs for new taxa"),
HTML(
"<p><em>Taxonomy file for new taxa has to be a tab-delimited
text file and has the following header (please follow the rule
above):</em></p><p>ncbiID fullName rank
parentID</p>"
),
bsAlert("wrong_new_taxa"),
hr(),
shinyBS::bsButton("new_done", "Finish adding", style = "warning",
disabled = TRUE)
),
# * popup for confirming parsing taxa from input file ------------------
bsModal(
"parse_confirm",
"Get taxonomy info",
"but_parse",
size = "small",
HTML(
'<p>Fetching Missing Taxonomy Information and
Post-processing.</p><p><em>This windows will close
automatically when eveything is done. Please wait...</em></p>
<p><strong><span style="color: #ff0000;">PLEASE RELOAD THIS
TOOL WHEN FINISHED!!!</span></strong></p>'
)
),
# * popup for plotting detailed plot -----------------------------------
bsModal(
"modal_bs",
"Detailed plot",
"detailed_btn",
size = "large",
fluidRow(
column(
2,
create_plot_size("detailed_height", "Height (px)", 100)
),
column(
3,
create_text_size("detailed_text", "Text size (px)", 12, 150)
),
column(
7,
checkboxInput(
"detailed_remove_na",
strong("Hide taxa that have no ortholog (NAs)",
style = "color:red"),
value = FALSE
)
)
),
hr(),
create_detailed_plot_ui("detailed_plot"),
shinyBS::bsButton("do_domain_plot",
"Show domain architecture",
disabled = TRUE),
uiOutput("check_domain_files"),
br(),
h4("Sequence:"),
verbatimTextOutput("fasta")
),
# * popup for plotting domain architecture plot ------------------------
bsModal(
"plot_archi",
"Domain architecture",
"do_domain_plot",
size = "large",
fluidRow(
column(
2,
create_plot_size("archi_height", "Plot height(px)", 400)
),
column(
2,
create_plot_size("archi_width", "Plot width(px)", 800)
),
column(
2,
create_text_size("title_archi_size", "Title size(px)",
11, 150)
),
column(
2,
create_text_size("label_archi_size", "SeqID size(px)",
11, 150)
)
),
uiOutput("test.ui"),
create_architecture_plot_ui("archi_plot")
),
# * popup for setting plot colors (profiles) ---------------------------
bsModal(
"color",
"Set colors for profile",
"set_color",
size = "small",
colourpicker::colourInput(
"low_color_var1",
"Low variable 1 (dot)",
value = "darkorange"
),
colourpicker::colourInput(
"high_color_var1",
"High variable 1 (dot)",
value = "steelblue"
),
actionButton(
"default_color_var1",
"Default",
style = "padding:4px; font-size:100%"
),
hr(),
colourpicker::colourInput(
"low_color_var2",
"Low variable 2 (background)",
value = "grey95"
),
colourpicker::colourInput(
"high_color_var2",
"High variable 2 (background)",
value = "khaki"
),
actionButton(
"default_color_var2",
"Default",
style = "padding:4px; font-size:100%"
),
hr(),
colourpicker::colourInput(
"para_color",
"Color for inparalogs",
value = "#07d000"
),
actionButton(
"default_color_para",
"Default",
style = "padding:4px; font-size:100%"
)
),
# * popup for FASTA upload ---------------------------------------------
bsModal(
"fasta_upload_bs",
"FASTA upload",
"fasta_upload",
size = "small",
selectInput(
"input_type", "Choose location for:",
c("Concatenated fasta file", "Fasta folder")
),
hr(),
uiOutput("default_color_para.ui"),
conditionalPanel(
condition = "input.input_type == 'Concatenated fasta file'",
fileInput("concat_fasta", ""),
uiOutput("concat_fasta.exist_check")
),
conditionalPanel(
condition = "input.input_type == 'Fasta folder'",
textInput("path", "Main FULL path:", ""),
selectInput(
"dir_format", "Directory format:",
choices = list("path/speciesID.fa*" = 1,
"path/speciesID/speciesID.fa*" = 2),
selected = "Path/speciesID.fasta"
),
selectInput(
"file_ext", "File extension:",
choices = list("fa" = "fa",
"fasta" = "fasta",
"fas" = "fas",
"txt" = "txt"),
selected = "fa"
),
selectInput(
"id_format",
"ID format:",
choices = list(">speciesID:seqID" = 1,
">speciesID@seqID" = 2,
">speciesID|seqID" = 3,
">seqID" = 4),
selected = 4
)
)
),
# * popup for upload gene category -------------------------------------
bsModal(
"upload_gene_category_bs",
"Upload gene categories",
"upload_gene_category",
size = "small",
fileInput("gene_category", "")
),
# * popup for setting Main plot configurations -------------------------
bsModal(
"main_plot_config_bs",
"Plot appearance configuration",
"main_plot_config",
size = "small",
column(
6,
create_text_size("x_size", "X-axis label size (px)", 8, 100)
),
column(
6,
create_text_size("y_size", "Y-axis label size (px)", 8, 100)
),
column(
6,
create_text_size("legend_size", "Legend label size (px)",
8, 150)
),
column(
6,
selectInput(
"main_legend", label = "Legend position:",
choices = list("Right" = "right",
"Left" = "left",
"Top" = "top",
"Bottom" = "bottom",
"Hide" = "none"),
selected = "right",
width = 150
)
),
column(
12,
HTML("<strong>Angle for x-axis label</strong>:<br>"),
sliderInput(
"x_angle",
"",
min = 0,
max = 90,
step = 10,
value = 60,
width = 250
),
br()
),
column(
12,
HTML("<strong>Zooming factor (α) for dots on
profile</strong>:<br>"),
sliderInput(
"dot_zoom", "",
min = -1,
max = 3,
step = 0.1,
value = 0,
width = 250
),
HTML("<em>dot size = (1+α)*default_size<br>default_size
=[0:5]</em>"),
uiOutput("dot_size_info"),
br()
),
br(),
hr(),
shinyBS::bsButton("reset_main_config", "Reset", style = "danger"),
shinyBS::bsButton("applyMainConfig", "Done", style = "warning")
),
# * popup for setting Customized plot configurations -------------------
bsModal(
"selected_plot_config_bs",
"Plot appearance configuration",
"selected_plot_config",
size = "small",
column(
6,
create_text_size("x_size_select", "X-axis label size (px)",
8, 100)
),
column(
6,
create_text_size("y_size_select", "Y-axis label size (px)",
8, 100)
),
column(
6,
create_text_size("legend_size_select", "Legend label size (px)",
8, 150)
),
column(
6,
selectInput(
"selected_legend", label = "Legend position:",
choices = list("Right" = "right",
"Left" = "left",
"Top" = "top",
"Bottom" = "bottom",
"Hide" = "none"),
selected = "right",
width = 150
)
),
column(
12,
HTML("<strong>Angle for x-axis label</strong>:<br>"),
sliderInput(
"x_angle_select", "",
min = 0,
max = 90,
step = 10,
value = 60,
width = 250
),
br()
),
column(
12,
HTML("<strong>Zooming factor (α) for dots on
profile</strong>:<br>"),
sliderInput(
"dot_zoom_select", "",
min = -1,
max = 3,
step = 0.1,
value = 0,
width = 250
),
HTML("<em>dot size = (1+α)*default_size<br>
default_size=[0:5]</em>"),
uiOutput("dot_size_infoSelect"),
br()
),
br(),
hr(),
shinyBS::bsButton("reset_selected_config", "Reset",
style = "danger"),
shinyBS::bsButton("apply_selected_config", "Done",
style = "warning")
),
# * popup for setting Gene age plot configurations ---------------------
bsModal(
"gene_age_prot_config_bs",
"Plot appearance configuration",
"gene_age_prot_config",
size = "small",
sliderInput(
"gene_age_width",
"Width zoom (*600px)",
min = 0,
max = 5,
step = 0.1,
value = 1,
width = "100%"
),
sliderInput(
"gene_age_height", "Height zoom (*150px)",
min = 0,
max = 5,
step = 0.1,
value = 1,
width = "100%"
),
sliderInput(
"gene_age_text", "Text size zoom",
min = 0,
max = 5,
step = 0.1,
value = 1,
width = "100%"
),
br(),
hr(),
shinyBS::bsButton(
"reset_gene_age_prot_config",
"Reset",
style = "danger"
)
),
# * popup for setting Group compariosn plot configurations -------------
bsModal(
"gc_plot_config_bs",
"Plot appearance configuration",
"gc_plot_config",
size = "small",
column(
6,
create_text_size("x_size_gc", "X-axis label size (px)", 10, 100)
),
column(
6,
create_text_size("y_size_gc", "Y-axis label size (px)", 10, 100)
),
column(
6,
create_text_size("legend_size_gc", "Legend label size (px)",
10, 150)
),
column(
6,
selectInput(
"legend_gc", label = "Legend position:",
choices = list("Right" = "right",
"Left" = "left",
"Top" = "top",
"Bottom" = "bottom",
"Hide" = "none"),
selected = "right",
width = 150
)
),
column(
6,
create_text_size("p_values_size_gc", "P-value label size (px)",
10, 100)
),
column(
6,
selectInput(
"show_point_gc", label = "Show location parameter:",
choices = list("Mean" = "mean",
"Median" = "median"),
selected = "mean",
width = 150)
),
column(
12,
sliderInput(
"angle_gc", "Angle of the X-axis label",
min = 0,
max = 180,
step = 1,
value = 90,
width = 250
)
),
column(
12,
checkboxInput(
"show_p_value",
strong("Show P-Values"),
value = TRUE,
width = 250
)
),
column(
12,
popify(
checkboxInput(
"highlight_significant",
strong("Highlight significant plots"),
value = TRUE,
width = 250
),
"",
"If both variables are selected the significant plot
is colored"
)
),
br(),
hr(),
shinyBS::bsButton("reset_config_gc", "Reset", style = "danger"),
shinyBS::bsButton("apply_config_gc", "Done", style = "warning")
),
# * popup for select taxa on Customized Profile ------------------------
bsModal(
"cus_taxa_bs",
"Select taxon/taxa of interest",
"cus_taxa",
size = "small",
select_taxon_rank_ui("select_taxon_rank"),
checkboxInput(
"apply_cus_taxa",
strong("Apply to customized profile",
style = "color:red"),
value = FALSE
)
),
# * popup for select taxa on Core gene finding -------------------------
bsModal(
"browse_taxa_core_bs",
"Select taxon/taxa of interest",
"browse_taxa_core",
size = "small",
select_taxon_rank_ui("select_taxon_rank_core"),
checkboxInput(
"apply_core_taxa",
strong("Apply", style = "color:red"),
value = FALSE
)
),
# * popup for select taxa on Group comparison --------------------------
bsModal(
"taxa_gc_bs",
"Select taxon/taxa of interest",
"taxa_gc",
size = "small",
select_taxon_rank_ui("select_taxon_rank_gc"),
checkboxInput(
"apply_taxa_gc",
strong("Apply",
style = "color:red"),
value = FALSE
)
),
# POINT INFO BOX =======================================================
conditionalPanel(
condition =
"input.tabs=='Main profile' ||
input.tabs=='Customized profile'",
absolutePanel(
bottom = 5, left = 30,
fixed = TRUE,
draggable = TRUE,
h5("Point's info:"),
verbatimTextOutput("point_info"),
conditionalPanel(
condition = "output.point_info_status == 0",
shinyBS::bsButton(
"detailed_btn",
"Detailed plot",
style = "success",
disabled = FALSE
)
),
style = "opacity: 0.80"
)
)
)
)
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