R/webApp/ui.R
In TeamPerie/CellDestiny: An RShiny application for the visualization and analysis of single cell lineage-tracing data
Defines functions
ui_myApp
library(shiny)
library(shinydashboard)
library(shinyWidgets)
library(shinycustomloader)
ui_myApp<-function() {
dashboardPage(
#https://stackoverflow.com/questions/54146804/how-to-prevent-code-for-adding-an-image-to-shinydashboard-header-appearing-in-br
skin = "blue",
dashboardHeader(title = "CellDestiny"),
dashboardSidebar(
sidebarUserPanel( name = "Institut Curie",
image="data:image/jpeg;base64,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"
),
sidebarMenu(id = "sidebarmenu",
menuItem("QC",tabName = "QC", icon = icon('th'), selected = TRUE,
menuSubItem("Load Data", tabName = "load_QC"),
menuSubItem("Duplicates", tabName = "duplicats"),
menuSubItem("Repeat Use", tabName = "repeat_use")),
menuItem("Analysis", tabName = "Analysis" , icon = icon('chart-bar'),
menuSubItem("Load Data", tabName = "load_data"),
menuSubItem("Sample similarities", tabName = "sample_similaritiesMenu"),
menuSubItem("Clone size", tabName = "clone_sizeMenu"),
menuSubItem("Barcode sharing", tabName = "barcode_sharingMenu"),
menuSubItem("Diversity", tabName = "diversityMenu"),
menuSubItem("Categorisation", tabName = "categorisationMenu"))
)
), # end of dashboardSidebar
dashboardBody(
# change title police
tags$head(tags$style(HTML('
.main-header .logo {
font-family: "Garamond", sans-serif;
font-size: 30px;
}'
))),
tags$head(
tags$style(HTML(".main-sidebar {font-size: 15px}" ))
),
fluidPage(
#------------------------------#
#------- Set input files ------#
#------------------------------#
############### QC ******************************************************************************************************************
tabItems(
tabItem(tabName = "load_QC",
fluidRow(
## Get matrix
box(width = 12, title="Duplicate Matrix",status = "primary", solidHeader = TRUE,
radioButtons("replicats_matrix_extention", label = "Select your file extension : ",
inline = TRUE,
choices = c("csv", "csv2", "tsv"),
selected = NULL),
fileInput(inputId="replicats_matrix", label = 'Upload your barcode matrix composed of duplicated samples:',
accept = c(".csv", ".csv2",".tsv", ".csv.gz", ".csv2.gz",".tsv.gz"), multiple = FALSE),
dataTableOutput("contents_matQC"),
footer = "Accepted formarts: .csv (sep=','), .csv2 (sep=';') or .tsv (sep=tabulations) with corresponding separators"),
## Get metadata
box(width = 12,title ="Duplicate Metadata",status = "primary", solidHeader = TRUE,
radioButtons("replicats_metadata_extention", label = "Select your file extension : ",
inline = TRUE,
choices = c("csv", "csv2", "tsv"),
selected = NULL),
fileInput(inputId="replicats_metadata",label = 'Upload the metadata corresponding to your barcode matrix with duplicates:',
accept = c(".csv", ".csv2",".tsv", ".csv.gz", ".csv2.gz",".tsv.gz"), multiple = FALSE),
dataTableOutput("contents_metQC"),
footer = "Accepted formarts: .csv (sep=','), .csv2 (sep=';') or .tsv (sep=tabulations) with corresponding separators"),
## Get duplicate variable name
box(width = 4, title="Duplicate variable", status="primary", solidHeader=TRUE,
pickerInput(inputId = "replicats_var",
multiple = FALSE,
choices = NULL,
label = "Select the variable which defines your duplicates:",
options = pickerOptions(actionsBox = FALSE,
title = "Variable",
liveSearch = TRUE,
liveSearchStyle = "contains"))),
# test data
box(title ="Load test dataset",status = "warning", solidHeader = TRUE,
radioButtons(inputId ="QC_testdataLoder",
label = "Do you want to load test data ?",
choices = c("No", "Yes"),
selected = "No"),
tags$script(HTML("Shiny.addCustomMessageHandler('upload_txt_matQC', function(txt) {
var target = $('#replicats_matrix').parent().parent().parent().find('input[type=text]');
target.val(txt);
}); ")),
tags$script(HTML("Shiny.addCustomMessageHandler('upload_txt_metQC', function(txt) {
var target = $('#replicats_metadata').parent().parent().parent().find('input[type=text]');
target.val(txt);
}); "))
),
) # end of fluidRow
#)
), # end of conditionalPannel QC
############### ANALYSIS ******************************************************************************************************************
#tabItems(
tabItem(tabName = "load_data",
fluidRow(
## Get matrix
box(width = 12, title="Filtred Matrix",status = "primary", solidHeader = TRUE,
radioButtons("matrix_extention", label = "Select your file extension : ",
inline = TRUE,
choices = c("csv", "csv2", "tsv"),
selected = NULL),
fileInput(inputId="matrix",label = "Upload your filtered matrix:",
accept = c(".csv", ".csv2",".tsv", ".csv.gz", ".csv2.gz",".tsv.gz"),
multiple = FALSE),
dataTableOutput("contents_mat"),
footer = "Accepted formarts: .csv (sep=','), .csv2 (sep=';') or .tsv (sep=tabulations) with corresponding separators"),
## Get metadata
box(width = 12,title ="Metadata",status = "primary", solidHeader = TRUE,
radioButtons("metadata_extention", label = "Select your file extension : ",
inline = TRUE,
choices = c("csv", "csv2", "tsv"),
selected = NULL),
fileInput(inputId="metadata",label = "Upload the metadata corresponding to your filtred matrix:",
accept = c(".csv", ".csv2",".tsv", ".csv.gz", ".csv2.gz",".tsv.gz"),
multiple = FALSE),
dataTableOutput("contents_met"),
footer = "Accepted formarts: .csv (sep=','), .csv2 (sep=';') or .tsv (sep=tabulations) with corresponding separators"),
box(width = 4, title="Individuals", status="primary", solidHeader=TRUE,
pickerInput(inputId = "organism",
multiple = FALSE,
choices = NULL,
label = "Select the variable defining your individuals:",
options = pickerOptions(actionsBox = TRUE,
title = "ex: Mouse, Patients, etc.",
liveSearch = TRUE,
liveSearchStyle = "contains"))),
# test data
box(title ="Load test dataset",status = "warning", solidHeader = TRUE,
radioButtons(inputId ="Analysis_testdataLoder",
label = "Do you want to load test data ?",
choices = c("No", "Yes"),
selected = "No"),
tags$script(HTML(" Shiny.addCustomMessageHandler('upload_txt_mat', function(txt) {
var target = $('#matrix').parent().parent().parent().find('input[type=text]');
target.val(txt);
}); ")),
tags$script(HTML("Shiny.addCustomMessageHandler('upload_txt_met', function(txt) {
var target = $('#metadata').parent().parent().parent().find('input[type=text]');
target.val(txt);
}); "))
),
) # end of fluidRow
#)
), # end of conditionalPannel Analysis
############### Sub Menus ******************************************************************************************************************
#°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°
#tabItems(
tabItem(tabName = "duplicats",
fluidRow(
box(status = "primary", solidHeader = FALSE, width = "100%",
# Left column == questions box
column(width=4,
box(width = NULL, status ="primary",solidHeader = TRUE, title="Sample selections",
pickerInput(inputId = "varRep",
label = "Which variable(s) do you want to select your samples on?",
choices = NULL,
multiple = TRUE,
options = pickerOptions(actionsBox = TRUE,
title = "Variables",
liveSearch = TRUE,
liveSearchStyle = "contains")),
conditionalPanel("input.varRep!=''",
pickerInput(inputId = "valRep",
label = "Select value(s) take by variable(s):",
choices = NULL,
multiple = TRUE,
options = pickerOptions(actionsBox = TRUE,
title = "Values",
liveSearch = TRUE,
liveSearchStyle = "contains"))
)
), # end of sample selection box
box(width = NULL, status ="primary",solidHeader = TRUE, title="Graph options",
box(width = NULL, status ="primary",height = NULL,solidHeader = TRUE,
radioButtons(inputId = "QCtransformation",
label = "Which transformation do you want to apply? ", inline = TRUE,
selected = "arcsin",
choices = c("arcsin", "log10(x+1)", "none"))
),
box(width = NULL, status ="primary",height = NULL,solidHeader = TRUE,
radioButtons(inputId = "QCtransformation",
label = "Which transformation do you want to apply? ", inline = TRUE,
selected = "arcsin",
choices = c("arcsin", "log10(x+1)", "none"))
),
box(width = NULL, status ="primary",height = NULL,solidHeader = TRUE,
radioButtons(inputId = "correlDup",
label = "Choose your correlation method :", inline = TRUE,
choices = c("spearman", "pearson"),
selected = "pearson")
)
)
), # end of column user questions
column(width=8, align="center",
box(align="center", width = "100%", height = "100%",
conditionalPanel("input.valRep.length==0",
imageOutput("QCDotEx"), width="100%", height="100%"),
conditionalPanel("input.valRep.length>0",
uiOutput("plots"),
downloadButton("downloadImage_QC", "Plot"),
downloadButton("downloadTable_QC", "Matrix")
)
)
) # end of left column
) # end of box
)# end of fluid row
), # end of tabItem duplicats
#°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°
tabItem(tabName = "repeat_use",
fluidRow(
box(status = "primary", solidHeader = FALSE, width = "100%",
# Left column == questions box
column(width=4,
box(width = NULL, status ="primary",solidHeader = TRUE, title="Sample selections",
pickerInput(inputId = "indiv_varRU",
label = "Select the variable which defines your individuals:",
choices = NULL,
multiple = FALSE,
options = pickerOptions(actionsBox = TRUE,
title = "Individuals",
liveSearch = FALSE,
liveSearchStyle = "contains")),
conditionalPanel("input.indiv_varRU!=''",
pickerInput(inputId = "indiv_valRU",
label = "Which individuals do you want to plot ?",
choices = NULL,
multiple = TRUE,
options = pickerOptions(actionsBox = TRUE,
title = "Values",
liveSearch = TRUE,
liveSearchStyle = "contains"))
)
) # end of sample selection box
), # end of column user questions
column(width=8, align="center",
box(align="center", width = "100%", height = "100%",
conditionalPanel("input.indiv_valRU.length==0",
imageOutput("RUDotEx"), width="100%", height="100%"),
conditionalPanel("input.indiv_valRU.length>0",
uiOutput("plotsRU"),
downloadButton("downloadImage_RU", "Plot"),
downloadButton("downloadTable_RU", "Matrix")
)
)
) # end of left column
) # end of box
)# end of fluid row
),# end of tabItem repeat_use
#°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°
##############################
#### Sample Similarities ###
##############################
tabItem(tabName = "sample_similaritiesMenu",
# Row of 2 big columns
fluidRow(
box(status = "primary", solidHeader = FALSE, width = "100%",
# Left column == questions box
column(width=4,
box(width = NULL, status ="primary", height = NULL, solidHeader = TRUE,
radioButtons(inputId = "graph_sampleSim",
label = "Select the type of graph:",
inline = FALSE,
choices = c("None", "Heatmap", "Correlogram"),
selected = 'None')
),
conditionalPanel(condition ="input.graph_sampleSim != 'None'",
box(width = NULL, title="Sample selections", status ="primary",solidHeader = TRUE,
box(width = NULL, status ="primary",solidHeader = TRUE,
pickerInput(inputId = "organismSample",
label = "Which individual(s) do you want to display ?",
choices = NULL,
multiple = TRUE,
options = pickerOptions(actionsBox = TRUE,
title = "Individuals",
liveSearch = TRUE,
liveSearchStyle = "contains"))
),
box(width = NULL, status ="primary",solidHeader = TRUE,
pickerInput(inputId = "variable",
label = "Which variable(s) do you want to display ?",
choices = NULL,
multiple = TRUE,
options = pickerOptions(actionsBox = TRUE,
title = "Variables",
liveSearch = TRUE,
liveSearchStyle = "contains")),
pickerInput(inputId = "value",
label= "Select at least two values to plot with:",
multiple = TRUE,
choices = NULL,
options = pickerOptions(actionsBox = TRUE,
title = "Values",
liveSearch = TRUE,
liveSearchStyle = "contains"))
)
) # end of Sample selections
), # end of none
#### Heatmap options ####
##########################
conditionalPanel("input.value.length>0 && input.graph_sampleSim == 'Heatmap'",
box(width = NULL, title="Graph options", status ="primary",solidHeader = TRUE,
box(width = NULL, status ="primary",height = NULL,solidHeader = TRUE,
radioButtons(inputId = "changeCalcul",
label = "Do you want to change default distance and clustering methods?", inline = TRUE,
choices = c("no", "yes"),
selected = "no")),
conditionalPanel("input.changeCalcul=='yes'",
box(width = NULL, status ="primary",height = NULL,solidHeader = TRUE,
radioButtons(inputId = "distance",
label = "Which distance method do you want?", inline = TRUE,
choices = c("euclidean", "maximum", "manhattan", "canberra"),
selected = "euclidean")),
box(width = NULL, status ="primary",height = NULL,solidHeader = TRUE,
# https://support.minitab.com/en-us/minitab/18/help-and-how-to/modeling-statistics/multivariate/how-to/cluster-observations/methods-and-formulas/linkage-methods/
radioButtons(inputId = "clustering",
label = "Which clustering method do you want?", inline = TRUE,
choices = c("complete", "average", "mcquitty", "median", "centroid", "ward.D2"),
selected = "complete"))
), # end of changeCalcul=='yes'
box(width = NULL, status ="primary",height = NULL,solidHeader = TRUE,
radioButtons(inputId = "dendro",
label = "Do you want to display a column dendrogram?", inline = TRUE,
choices = c("no", "yes"),
selected = "no")),
box(width = NULL, status ="primary",height = NULL,solidHeader = TRUE,
uiOutput("nclustersUi")
),
box(width = NULL, status ="primary",height = NULL,solidHeader = TRUE,
radioButtons(inputId = "barcodes",
label = "Do you want to display a row barcodes?", inline = TRUE,
choices = c("no", "yes"),
selected = "no"))
) # end of graph options
) # end of conditionalPanel Heatmap
),
#), # end of left column
# Rigth column == Plot box
column(width=8, align="center",
###################
#### Heatmap ####
###################
conditionalPanel("input.graph_sampleSim=='Heatmap'",
tabBox(height="100%", width = "100%",
title = "",
id = "tabHeatmap",
tabPanel(id="tabFig",
title="Figure",
conditionalPanel("input.value.length==0",
imageOutput("heatmapEx", width="100%")),
conditionalPanel("input.value.length>0",
plotOutput(outputId="heatmap")),
conditionalPanel("input.value.length>0",
downloadButton("downloadImage_heatmap", "Plot"),
downloadButton("downloadTable_heatmap", "Matrix"))
),
tabPanel(id="tabInfo",
title="Details",
"Used distance: ",
conditionalPanel("input.value.length==0 ",
verbatimTextOutput("distanceEx")),
conditionalPanel("input.value.length>0 ",
verbatimTextOutput("distanceSelected")),
"Used clustering: ",
conditionalPanel("input.value.length==0 ",
verbatimTextOutput("clusteringEx")),
conditionalPanel("input.value.length>0 ",
verbatimTextOutput("clusteringSelected")))
) # end of tabBox
), # end of conditionalPanel heatmap
#######################
#### Correlogram ####
#######################
conditionalPanel("input.graph_sampleSim=='Correlogram'",
box(width = NULL, title="Graph options", status ="primary",solidHeader = TRUE,
box(width = NULL, status ="primary",height = NULL,solidHeader = TRUE,
radioButtons(inputId = "correlation",
label = "Choose your correlation method :", inline = TRUE,
choices = c("spearman", "pearson"),
selected = "pearson"))),
box(align="center", width = "100%", height = "100%",
#uiOutput("CloneSizeUI"),
conditionalPanel("input.value.length==0 ",
imageOutput("correloEx")),
conditionalPanel("input.value.length>0 ",
plotOutput(outputId="correlo"),
downloadButton("downloadImage_correlo", "Plot"),
downloadButton("downloadTable_correlo", "Matrix"))
)
) # end of condit panel Correlogram
)# end of right column
) # end of big box
) # end of fluidrow
), # end of tabItem sample_similaritiesMenu
#°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°
#####################
#### Clone size ###
#####################
tabItem(tabName = "clone_sizeMenu",
# Row of 2 big columns
fluidRow(
box(status = "primary", solidHeader = FALSE, width = "100%",
# Left column == questions box
column(width=4,
box(width = NULL, status ="primary",height = NULL,solidHeader = TRUE,
radioButtons(inputId = "graphType2",
label = "Select the type of graph:", inline = FALSE,
selected = "None",
choices = c("None", "Cumulative diagram", "Frequency distribution"))
),
conditionalPanel("input.graphType2!='None'",
box(width = NULL, title="Sample selections", status ="primary",solidHeader = TRUE,
box(width = NULL, status ="primary",solidHeader = TRUE,
pickerInput(inputId = "organismSampleCS",
label = "Which individual(s) do you want to display ?",
choices = NULL,
multiple = TRUE,
options = pickerOptions(actionsBox = TRUE,
title = "Individuals",
liveSearch = TRUE,
liveSearchStyle = "contains"))
),
box(width = NULL, status ="primary",height = 200,solidHeader = TRUE,
pickerInput(inputId = "variableCS",
label = "Which variable(s) do you want to display ?",
choices = NULL,
multiple = TRUE,
options = pickerOptions(actionsBox = TRUE,
title = "Variables",
liveSearch = TRUE,
liveSearchStyle = "contains")),
pickerInput(inputId = "valueCS",
label= "Select the value(s) take by variable(s):",
multiple = TRUE,
choices = NULL,
options = pickerOptions(actionsBox = TRUE,
title = "Values",
liveSearch = TRUE,
liveSearchStyle = "contains"))
)), # end of sample selection
box(width = NULL, title="Graph option", status ="primary",solidHeader = TRUE,
conditionalPanel("input.graphType2=='Frequency distribution'",
box(width = NULL, status ="primary",solidHeader = TRUE,
radioButtons(inputId = "yCS",
label= "Select the type of diagram:",
choices = c("Density curve", "Histogarm"),
selected = "Density curve",
inline = FALSE))
),
box(width = NULL, status ="primary",solidHeader = TRUE,
radioButtons(inputId = "doColor",
label= "Do you want to add colors :",
choices = c("no", "yes"),
selected = "no",
inline = FALSE),
conditionalPanel("input.doColor=='yes'",
pickerInput(inputId = "colorCS",
label= "Select the variable for the color:",
multiple = FALSE,
choices = NULL,
options = pickerOptions(actionsBox = FALSE,
title = "Color",
liveSearch = TRUE,
liveSearchStyle = "contains"))
)
),
# only freq
conditionalPanel("input.graphType2=='Frequency distribution'",
box(width = NULL, status ="primary",solidHeader = TRUE,
sliderInput("nbins", label = "Select a number of bins", min = 0,
max = 100, value = 5))
),
# only cum
conditionalPanel("input.graphType2=='Cumulative diagram'",
box(width = NULL, status ="primary",solidHeader = TRUE,
radioButtons(inputId ="xProportion",
label = "Convert x axis in percentage :",
choices = c("no", "yes"),
selected = "no",
inline = FALSE))
)
) # end of graph option
)
), #end of left box
column(width=8, align="center",
box(align="center", width = "100%", height = "100%",
## Clone Size ##
#°°°°°°°°°°°°°°°°°°°°°°°°#
#uiOutput("CloneSizeUI"),
conditionalPanel("input.graphType2=='Cumulative diagram' && input.valueCS.length==0 ",
imageOutput("cumulativeDiagramEx")),
conditionalPanel("input.graphType2=='Cumulative diagram' && input.valueCS.length>0 ",
plotOutput(outputId="cumulativeDiagram"),
downloadButton("downloadImage_cumDiag", "Plot"),
downloadButton("downloadTable_cumDiag", "Matrix")
),
conditionalPanel("input.graphType2=='Frequency distribution' && input.valueCS.length==0",
imageOutput("nonCumulativeHistEx")),
conditionalPanel("input.graphType2=='Frequency distribution' && input.valueCS.length>0 ",
plotOutput(outputId="nonCumulativeHist"),
downloadButton("downloadImage_nonCumHist", "Plot"),
downloadButton("downloadTable_nonCumHist", "Matrix")
)
) # end of right box
) # end of right column
) # end of big box
) # end of fluidrow
), # end of tabItem clone size
#°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°
##########################
#### Barcode sharing ###
#########################
tabItem(tabName = "barcode_sharingMenu",
# Row of 2 big columns
fluidRow(
box(status = "primary", solidHeader = FALSE, width = "100%",
# Left column == questions box
column(width=4,
box(width = NULL, status ="primary",height = NULL,solidHeader = TRUE,
radioButtons(inputId = "graphType1",
label = "Select the type of graph:", inline = FALSE,
selected = "None",
choices = c("None", "Dotplot", "Ternary plot"))
),
conditionalPanel("input.graphType1!='None'",
box(width = NULL, title="Sample selections", status ="primary",solidHeader = TRUE,
box(width = NULL, status ="primary",solidHeader = TRUE,
pickerInput(inputId = "organismSampleSB",
label = "Which individual(s) do you want to display ?",
choices = NULL,
multiple = TRUE,
options = pickerOptions(actionsBox = TRUE,
title = "Individuals",
liveSearch = TRUE,
liveSearchStyle = "contains"))
),
conditionalPanel("input.graphType1=='Dotplot'",
box(width = NULL,title="x axis", status ="primary",solidHeader = TRUE,
pickerInput(inputId = "x_var",
label = "Select x variable(s):",
choices = NULL,
multiple = TRUE,
options = pickerOptions(actionsBox = TRUE,
title = "Variables",
liveSearch = TRUE,
liveSearchStyle = "contains")),
pickerInput(inputId = "x_val",
label = "Select x value(s) to display:",
choices = NULL,
multiple = TRUE,
options = pickerOptions(actionsBox = TRUE,
title = "Values",
liveSearch = TRUE,
liveSearchStyle = "contains"))
),
box(width = NULL,title="y axis", status ="primary",solidHeader = TRUE,
pickerInput(inputId = "y_var",
label = "Select y variable(s):",
choices = NULL,
multiple = TRUE,
options = pickerOptions(actionsBox = TRUE,
title = "Variables",
liveSearch = TRUE,
liveSearchStyle = "contains")),
pickerInput(inputId = "y_val",
label = "Select y value(s) to display:",
choices = NULL,
multiple = TRUE,
options = pickerOptions(actionsBox = TRUE,
title = "Values",
liveSearch = TRUE,
liveSearchStyle = "contains"))
)), # end of conditionalPanel Dotplot
conditionalPanel("input.graphType1=='Ternary plot'",
box(width = NULL,title="Value1", status ="primary",solidHeader = TRUE,
pickerInput(inputId = "top_var",
label= "Select variable(s):",
multiple = TRUE,
choices = NULL,
options = pickerOptions(actionsBox = TRUE,
title = "Variables",
liveSearch = TRUE,
liveSearchStyle = "contains")),
pickerInput(inputId = "top_val",
label= "Select values(s) to display (left axis):",
multiple = TRUE,
choices = NULL,
options = pickerOptions(actionsBox = TRUE,
title = "Values",
liveSearch = TRUE,
liveSearchStyle = "contains"))
),
box(width = NULL,title="Value2", status ="primary",solidHeader = TRUE,
pickerInput(inputId = "right_var",
label= "Select variable(s):",
multiple = TRUE,
choices = NULL,
options = pickerOptions(actionsBox = TRUE,
title = "Variables",
liveSearch = TRUE,
liveSearchStyle = "contains")),
pickerInput(inputId = "right_val",
label= "Select values(s) to display (right axis):",
multiple = TRUE,
choices = NULL,
options = pickerOptions(actionsBox = TRUE,
title = "Values",
liveSearch = TRUE,
liveSearchStyle = "contains"))
),
box(width = NULL,title="Value3", status ="primary",solidHeader = TRUE,
pickerInput(inputId = "left_var",
label= "Select variable(s):",
multiple = TRUE,
choices = NULL,
options = pickerOptions(actionsBox = TRUE,
title = "Variables",
liveSearch = TRUE,
liveSearchStyle = "contains")),
pickerInput(inputId = "left_val",
label= "Select values(s) to display (bottom axis):",
multiple = TRUE,
choices = NULL,
options = pickerOptions(actionsBox = TRUE,
title = "Values",
liveSearch = TRUE,
liveSearchStyle = "contains"))
)
) # end of conditional panel Ternary
), # end of sample selection
box(width = NULL, title="Graph options", status ="primary",solidHeader = TRUE,
conditionalPanel("input.graphType1=='Dotplot'",
box(width = NULL, status ="primary",height = NULL,solidHeader = TRUE,
radioButtons(inputId = "SBtransformation",
label = "Which transformation do you want to apply? ", inline = TRUE,
selected = "arcsin",
choices = c("arcsin", "log10(x+1)", "none"))
)
),
conditionalPanel("input.graphType1=='Dotplot'",
box(width = NULL, status ="primary",height = NULL,solidHeader = TRUE,
radioButtons(inputId = "filledPlotSB",
label = "Do you want to color dots?", inline = TRUE,
selected = "no",
choices = c("no", "yes")),
conditionalPanel("input.filledPlotSB=='yes'" ,
pickerInput(inputId = "colorSB",
label= "Select the variable to color:",
multiple = FALSE,
choices = NULL,
options = pickerOptions(actionsBox = TRUE,
title = "Color",
liveSearch = FALSE))
)
)
),
conditionalPanel("input.graphType1=='Ternary plot'" ,
radioButtons(inputId = "colorSB_ternary",
label = "Do you want to color dots according individuals ?", inline = TRUE,
selected = "no",
choices = c("no", "yes")))
) # end of graph options
) #end of conditionalPanel not None
), # end of left column
column(width=8, align="center",
box(align="center", width = "100%", height = "100%",
conditionalPanel("input.graphType1=='Dotplot' && (input.x_val.length==0 || input.y_val.length==0) ",
imageOutput("dotplotEx")),
conditionalPanel("input.graphType1=='Dotplot' && input.x_val.length>0 && input.y_val.length>0 ",
# dotplot
plotOutput(outputId="dotplot"),
downloadButton("downloadImage_dotplot", "Plot"),
downloadButton("downloadTable_dotplot", "Matrix"),
# piechart plot
plotOutput(outputId="piechart"),
downloadButton("downloadImage_piechart", "Plot"),
downloadButton("downloadTable_piechart", "Matrix")),
conditionalPanel("input.graphType1=='Ternary plot' && (input.top_val.length==0 || input.left_val.length==0 || input.right_val.length==0)",
imageOutput("ternaryPlotEx")),
conditionalPanel("input.graphType1=='Ternary plot' && input.top_val.length>0 && input.left_val.length>0 && input.right_val.length>0",
plotOutput(outputId="ternaryPlot"),
downloadButton("downloadImage_ternary", "Plot"),
downloadButton("downloadTable_ternary", "Matrix"))
) # end of right box
) # end of right column
) # end of big box
) # end of fluidrow
), # end of tabItem barcode sharing
#°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°
####################
#### Diversity ###
####################
tabItem(tabName = "diversityMenu",
# Row of 2 big columns
fluidRow(
box(status = "primary", solidHeader = FALSE, width = "100%",
# Left column == questions box
column(width=4,
box(width = NULL, title="Sample selections", status ="primary",solidHeader = TRUE,
# changer pour le dotplot, proposer uniquement un seul choix pour la variable
box(width = NULL, status ="primary",solidHeader = TRUE,
pickerInput(inputId = "organismSample_notPooled",
label = "Select individual(s): ",
choices = NULL,
multiple = TRUE,
options = pickerOptions(actionsBox = TRUE,
title = "Individuals",
liveSearch = TRUE,
liveSearchStyle = "contains"))
),
box(width = NULL, status ="primary",solidHeader = TRUE,
pickerInput(inputId = "variable_notPooled",
label = "Select x axis variable(s):",
choices = NULL,
multiple = TRUE,
options = pickerOptions(actionsBox = TRUE,
title = "Variables",
liveSearch = TRUE,
liveSearchStyle = "contains")),
pickerInput(inputId = "value_notPooled",
label= "Select value(s) take by x axis variable(s):",
multiple = TRUE,
choices = NULL,
options = pickerOptions(actionsBox = TRUE,
title = "Values",
liveSearch = TRUE,
liveSearchStyle = "contains"))
),
box(width = NULL, status ="primary",solidHeader = TRUE,
radioButtons(inputId = "yBoxplot",
label = "What do you want in y axis ?", inline = TRUE,
selected = "Number of barcodes",
choices = c("Number of barcodes", "Shannon index", "Simpson index"))
)
), # end of box Sample selection
box(width = NULL, title="Graph options", status ="primary",solidHeader = TRUE,
box(width = NULL, status ="primary",solidHeader = TRUE,
radioButtons(inputId = "boxplotCondition",
label = "Do you want to color your plot ?", inline = TRUE,
selected = "no",
choices = c("no", "yes")),
conditionalPanel("input.boxplotCondition=='yes'",
pickerInput(inputId = "boxplotColor_var",
label= "Select a variable: ",
multiple = FALSE,
choices = NULL,
options = pickerOptions(actionsBox = FALSE,
title = "Variable",
liveSearch = FALSE))
)),
box(width = NULL, status ="primary",solidHeader = TRUE,
radioButtons(inputId = "boxplotDot",
label = "Do you want to display dots?", inline = TRUE,
selected = "no",
choices = c("no", "yes"))
)
) # end of Graph options
), # end of left column
column(width=8, align="center",
box(align="center", width = "100%", height = "100%",
conditionalPanel("input.value_notPooled.length<1",
imageOutput("boxplotEx")),
conditionalPanel("input.value_notPooled.length>=1",
plotOutput(outputId="boxplot"),
downloadButton("downloadImage_boxplot", "Plot"),
downloadButton("downloadTable_boxplot", "Matrix"))
) # end of right box
) # end of right column
) # end of big box
) # end of fluidrow
), # end of tabItem diversityMenu
#°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°
#########################
#### Categorisation ###
#########################
tabItem(tabName = "categorisationMenu",
# Row of 2 big columns
fluidRow(
box(status = "primary", solidHeader = FALSE, width = "100%",
# Left column == questions box
column(width=4,
box(width = NULL, status ="primary",height = NULL,solidHeader = TRUE,
radioButtons(inputId = "CatGraph",
label = "Select the analysis:", inline = FALSE,
selected = "None",
choices = c("None", "Category analysis", "Bias analysis"))
),
conditionalPanel("input.CatGraph!='None'",
box(width = NULL, status ="primary",solidHeader = TRUE, title="Sample selections",
pickerInput(inputId = "organismCat",
label = "Select individual(s):",
choices = NULL,
multiple = TRUE,
options = pickerOptions(actionsBox = TRUE,
title = "Individuals",
liveSearch = TRUE,
liveSearchStyle = "contains")),
pickerInput(inputId = "catVar",
label = "Select the variable used for cell types:",
choices = NULL,
multiple = FALSE,
options = pickerOptions(actionsBox = TRUE,
title = "Categorgy",
liveSearch = TRUE,
liveSearchStyle = "contains")),
conditionalPanel("input.catVar!=''",
pickerInput(inputId = "catVal",
label = "Select its values:",
choices = NULL,
multiple = TRUE,
options = pickerOptions(actionsBox = TRUE,
liveSearch = TRUE,
liveSearchStyle = "contains"))),
conditionalPanel("input.catVar!='' && input.catVal.length>1 && input.CatGraph=='Bias analysis'",
pickerInput(inputId = "yBias",
label = "Select one cell type:",
choices = NULL,
multiple = FALSE,
options = pickerOptions(actionsBox = TRUE,
liveSearch = TRUE,
liveSearchStyle = "contains")))
), # end of Sample selections
box(width = NULL, status ="primary",solidHeader = TRUE,title="Graph option",
conditionalPanel("input.CatGraph=='Category analysis'",
box(width = NULL, status ="primary",solidHeader = TRUE,title="Threshold value",
sliderInput("slider", label = "Select the threshold used for categorization:", min = 0,
max = 100, value = 20))),
radioButtons(inputId = "condition",
label = "Do you want to add a condition (e.g: treatment, organ, etc.) ? ", inline = TRUE,
selected = "no",
choices = c("no","yes")),
conditionalPanel("input.condition=='yes' && input.catVar!=''",
pickerInput(inputId = "conditionVal",
label = "Select your condition value:",
choices = NULL,
multiple = FALSE,
options = pickerOptions(actionsBox = TRUE,
title = "Condition",
liveSearch = TRUE,
liveSearchStyle = "contains")))
) # end of box Graph opt
) # end of conditional None
), # end of left column
column(width=8, align="center",
box(align="center", width = "100%", height = "100%",
conditionalPanel("input.CatGraph=='Category analysis'",
conditionalPanel("input.catVal.length<=1 && input.organismCat.length==0",
imageOutput("contrib2"),
imageOutput("contrib1")
)),
conditionalPanel("input.catVal.length>1 && input.organismCat.length>0 && input.CatGraph=='Category analysis'",
# first plot
withLoader(plotOutput(outputId="bargraphCat_counts"), type = "html", loader = "dnaspin"),
downloadButton("downloadImage_counts", "Plot"),
downloadButton("downloadTable_counts", "Matrix"),
# second plot
plotOutput(outputId="bargraphCat_percent"),
downloadButton("downloadImage_percent", "Plot"),
downloadButton("downloadTable_percent", "Matrix")
),
# print and export bias analysis graphs and matrices
conditionalPanel("input.catVal.length>1 && input.organismCat.length>0 && input.CatGraph=='Bias analysis'",
# first plot
withLoader(plotOutput(outputId="biasPerType"), type = "html", loader = "dnaspin"),
downloadButton("downloadImage_biasType", "Plot"),
downloadButton("downloadTable_biasType", "Matrix"),
# second plot
plotOutput(outputId="biasPerCat"),
downloadButton("downloadImage_biasCat", "Plot"),
downloadButton("downloadTable_biasCat", "Matrix")
)
) # end of right box
) # end of right column
) # end of big box
) # end of fluidrow
) # end of tabItem categorisationMenu
)# end of TabItems
)# end of fluidPage
)# end dashboardBody
)# end dashboardPage
}
TeamPerie/CellDestiny documentation built on July 4, 2022, 8:40 a.m.
R Package Documentation
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Defines functions ui_myApp
library(shiny)
library(shinydashboard)
library(shinyWidgets)
library(shinycustomloader)
ui_myApp<-function() {
dashboardPage(
#https://stackoverflow.com/questions/54146804/how-to-prevent-code-for-adding-an-image-to-shinydashboard-header-appearing-in-br
skin = "blue",
dashboardHeader(title = "CellDestiny"),
dashboardSidebar(
sidebarUserPanel( name = "Institut Curie",
image="data:image/jpeg;base64,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"
),
sidebarMenu(id = "sidebarmenu",
menuItem("QC",tabName = "QC", icon = icon('th'), selected = TRUE,
menuSubItem("Load Data", tabName = "load_QC"),
menuSubItem("Duplicates", tabName = "duplicats"),
menuSubItem("Repeat Use", tabName = "repeat_use")),
menuItem("Analysis", tabName = "Analysis" , icon = icon('chart-bar'),
menuSubItem("Load Data", tabName = "load_data"),
menuSubItem("Sample similarities", tabName = "sample_similaritiesMenu"),
menuSubItem("Clone size", tabName = "clone_sizeMenu"),
menuSubItem("Barcode sharing", tabName = "barcode_sharingMenu"),
menuSubItem("Diversity", tabName = "diversityMenu"),
menuSubItem("Categorisation", tabName = "categorisationMenu"))
)
), # end of dashboardSidebar
dashboardBody(
# change title police
tags$head(tags$style(HTML('
.main-header .logo {
font-family: "Garamond", sans-serif;
font-size: 30px;
}'
))),
tags$head(
tags$style(HTML(".main-sidebar {font-size: 15px}" ))
),
fluidPage(
#------------------------------#
#------- Set input files ------#
#------------------------------#
############### QC ******************************************************************************************************************
tabItems(
tabItem(tabName = "load_QC",
fluidRow(
## Get matrix
box(width = 12, title="Duplicate Matrix",status = "primary", solidHeader = TRUE,
radioButtons("replicats_matrix_extention", label = "Select your file extension : ",
inline = TRUE,
choices = c("csv", "csv2", "tsv"),
selected = NULL),
fileInput(inputId="replicats_matrix", label = 'Upload your barcode matrix composed of duplicated samples:',
accept = c(".csv", ".csv2",".tsv", ".csv.gz", ".csv2.gz",".tsv.gz"), multiple = FALSE),
dataTableOutput("contents_matQC"),
footer = "Accepted formarts: .csv (sep=','), .csv2 (sep=';') or .tsv (sep=tabulations) with corresponding separators"),
## Get metadata
box(width = 12,title ="Duplicate Metadata",status = "primary", solidHeader = TRUE,
radioButtons("replicats_metadata_extention", label = "Select your file extension : ",
inline = TRUE,
choices = c("csv", "csv2", "tsv"),
selected = NULL),
fileInput(inputId="replicats_metadata",label = 'Upload the metadata corresponding to your barcode matrix with duplicates:',
accept = c(".csv", ".csv2",".tsv", ".csv.gz", ".csv2.gz",".tsv.gz"), multiple = FALSE),
dataTableOutput("contents_metQC"),
footer = "Accepted formarts: .csv (sep=','), .csv2 (sep=';') or .tsv (sep=tabulations) with corresponding separators"),
## Get duplicate variable name
box(width = 4, title="Duplicate variable", status="primary", solidHeader=TRUE,
pickerInput(inputId = "replicats_var",
multiple = FALSE,
choices = NULL,
label = "Select the variable which defines your duplicates:",
options = pickerOptions(actionsBox = FALSE,
title = "Variable",
liveSearch = TRUE,
liveSearchStyle = "contains"))),
# test data
box(title ="Load test dataset",status = "warning", solidHeader = TRUE,
radioButtons(inputId ="QC_testdataLoder",
label = "Do you want to load test data ?",
choices = c("No", "Yes"),
selected = "No"),
tags$script(HTML("Shiny.addCustomMessageHandler('upload_txt_matQC', function(txt) {
var target = $('#replicats_matrix').parent().parent().parent().find('input[type=text]');
target.val(txt);
}); ")),
tags$script(HTML("Shiny.addCustomMessageHandler('upload_txt_metQC', function(txt) {
var target = $('#replicats_metadata').parent().parent().parent().find('input[type=text]');
target.val(txt);
}); "))
),
) # end of fluidRow
#)
), # end of conditionalPannel QC
############### ANALYSIS ******************************************************************************************************************
#tabItems(
tabItem(tabName = "load_data",
fluidRow(
## Get matrix
box(width = 12, title="Filtred Matrix",status = "primary", solidHeader = TRUE,
radioButtons("matrix_extention", label = "Select your file extension : ",
inline = TRUE,
choices = c("csv", "csv2", "tsv"),
selected = NULL),
fileInput(inputId="matrix",label = "Upload your filtered matrix:",
accept = c(".csv", ".csv2",".tsv", ".csv.gz", ".csv2.gz",".tsv.gz"),
multiple = FALSE),
dataTableOutput("contents_mat"),
footer = "Accepted formarts: .csv (sep=','), .csv2 (sep=';') or .tsv (sep=tabulations) with corresponding separators"),
## Get metadata
box(width = 12,title ="Metadata",status = "primary", solidHeader = TRUE,
radioButtons("metadata_extention", label = "Select your file extension : ",
inline = TRUE,
choices = c("csv", "csv2", "tsv"),
selected = NULL),
fileInput(inputId="metadata",label = "Upload the metadata corresponding to your filtred matrix:",
accept = c(".csv", ".csv2",".tsv", ".csv.gz", ".csv2.gz",".tsv.gz"),
multiple = FALSE),
dataTableOutput("contents_met"),
footer = "Accepted formarts: .csv (sep=','), .csv2 (sep=';') or .tsv (sep=tabulations) with corresponding separators"),
box(width = 4, title="Individuals", status="primary", solidHeader=TRUE,
pickerInput(inputId = "organism",
multiple = FALSE,
choices = NULL,
label = "Select the variable defining your individuals:",
options = pickerOptions(actionsBox = TRUE,
title = "ex: Mouse, Patients, etc.",
liveSearch = TRUE,
liveSearchStyle = "contains"))),
# test data
box(title ="Load test dataset",status = "warning", solidHeader = TRUE,
radioButtons(inputId ="Analysis_testdataLoder",
label = "Do you want to load test data ?",
choices = c("No", "Yes"),
selected = "No"),
tags$script(HTML(" Shiny.addCustomMessageHandler('upload_txt_mat', function(txt) {
var target = $('#matrix').parent().parent().parent().find('input[type=text]');
target.val(txt);
}); ")),
tags$script(HTML("Shiny.addCustomMessageHandler('upload_txt_met', function(txt) {
var target = $('#metadata').parent().parent().parent().find('input[type=text]');
target.val(txt);
}); "))
),
) # end of fluidRow
#)
), # end of conditionalPannel Analysis
############### Sub Menus ******************************************************************************************************************
#°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°
#tabItems(
tabItem(tabName = "duplicats",
fluidRow(
box(status = "primary", solidHeader = FALSE, width = "100%",
# Left column == questions box
column(width=4,
box(width = NULL, status ="primary",solidHeader = TRUE, title="Sample selections",
pickerInput(inputId = "varRep",
label = "Which variable(s) do you want to select your samples on?",
choices = NULL,
multiple = TRUE,
options = pickerOptions(actionsBox = TRUE,
title = "Variables",
liveSearch = TRUE,
liveSearchStyle = "contains")),
conditionalPanel("input.varRep!=''",
pickerInput(inputId = "valRep",
label = "Select value(s) take by variable(s):",
choices = NULL,
multiple = TRUE,
options = pickerOptions(actionsBox = TRUE,
title = "Values",
liveSearch = TRUE,
liveSearchStyle = "contains"))
)
), # end of sample selection box
box(width = NULL, status ="primary",solidHeader = TRUE, title="Graph options",
box(width = NULL, status ="primary",height = NULL,solidHeader = TRUE,
radioButtons(inputId = "QCtransformation",
label = "Which transformation do you want to apply? ", inline = TRUE,
selected = "arcsin",
choices = c("arcsin", "log10(x+1)", "none"))
),
box(width = NULL, status ="primary",height = NULL,solidHeader = TRUE,
radioButtons(inputId = "QCtransformation",
label = "Which transformation do you want to apply? ", inline = TRUE,
selected = "arcsin",
choices = c("arcsin", "log10(x+1)", "none"))
),
box(width = NULL, status ="primary",height = NULL,solidHeader = TRUE,
radioButtons(inputId = "correlDup",
label = "Choose your correlation method :", inline = TRUE,
choices = c("spearman", "pearson"),
selected = "pearson")
)
)
), # end of column user questions
column(width=8, align="center",
box(align="center", width = "100%", height = "100%",
conditionalPanel("input.valRep.length==0",
imageOutput("QCDotEx"), width="100%", height="100%"),
conditionalPanel("input.valRep.length>0",
uiOutput("plots"),
downloadButton("downloadImage_QC", "Plot"),
downloadButton("downloadTable_QC", "Matrix")
)
)
) # end of left column
) # end of box
)# end of fluid row
), # end of tabItem duplicats
#°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°
tabItem(tabName = "repeat_use",
fluidRow(
box(status = "primary", solidHeader = FALSE, width = "100%",
# Left column == questions box
column(width=4,
box(width = NULL, status ="primary",solidHeader = TRUE, title="Sample selections",
pickerInput(inputId = "indiv_varRU",
label = "Select the variable which defines your individuals:",
choices = NULL,
multiple = FALSE,
options = pickerOptions(actionsBox = TRUE,
title = "Individuals",
liveSearch = FALSE,
liveSearchStyle = "contains")),
conditionalPanel("input.indiv_varRU!=''",
pickerInput(inputId = "indiv_valRU",
label = "Which individuals do you want to plot ?",
choices = NULL,
multiple = TRUE,
options = pickerOptions(actionsBox = TRUE,
title = "Values",
liveSearch = TRUE,
liveSearchStyle = "contains"))
)
) # end of sample selection box
), # end of column user questions
column(width=8, align="center",
box(align="center", width = "100%", height = "100%",
conditionalPanel("input.indiv_valRU.length==0",
imageOutput("RUDotEx"), width="100%", height="100%"),
conditionalPanel("input.indiv_valRU.length>0",
uiOutput("plotsRU"),
downloadButton("downloadImage_RU", "Plot"),
downloadButton("downloadTable_RU", "Matrix")
)
)
) # end of left column
) # end of box
)# end of fluid row
),# end of tabItem repeat_use
#°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°
##############################
#### Sample Similarities ###
##############################
tabItem(tabName = "sample_similaritiesMenu",
# Row of 2 big columns
fluidRow(
box(status = "primary", solidHeader = FALSE, width = "100%",
# Left column == questions box
column(width=4,
box(width = NULL, status ="primary", height = NULL, solidHeader = TRUE,
radioButtons(inputId = "graph_sampleSim",
label = "Select the type of graph:",
inline = FALSE,
choices = c("None", "Heatmap", "Correlogram"),
selected = 'None')
),
conditionalPanel(condition ="input.graph_sampleSim != 'None'",
box(width = NULL, title="Sample selections", status ="primary",solidHeader = TRUE,
box(width = NULL, status ="primary",solidHeader = TRUE,
pickerInput(inputId = "organismSample",
label = "Which individual(s) do you want to display ?",
choices = NULL,
multiple = TRUE,
options = pickerOptions(actionsBox = TRUE,
title = "Individuals",
liveSearch = TRUE,
liveSearchStyle = "contains"))
),
box(width = NULL, status ="primary",solidHeader = TRUE,
pickerInput(inputId = "variable",
label = "Which variable(s) do you want to display ?",
choices = NULL,
multiple = TRUE,
options = pickerOptions(actionsBox = TRUE,
title = "Variables",
liveSearch = TRUE,
liveSearchStyle = "contains")),
pickerInput(inputId = "value",
label= "Select at least two values to plot with:",
multiple = TRUE,
choices = NULL,
options = pickerOptions(actionsBox = TRUE,
title = "Values",
liveSearch = TRUE,
liveSearchStyle = "contains"))
)
) # end of Sample selections
), # end of none
#### Heatmap options ####
##########################
conditionalPanel("input.value.length>0 && input.graph_sampleSim == 'Heatmap'",
box(width = NULL, title="Graph options", status ="primary",solidHeader = TRUE,
box(width = NULL, status ="primary",height = NULL,solidHeader = TRUE,
radioButtons(inputId = "changeCalcul",
label = "Do you want to change default distance and clustering methods?", inline = TRUE,
choices = c("no", "yes"),
selected = "no")),
conditionalPanel("input.changeCalcul=='yes'",
box(width = NULL, status ="primary",height = NULL,solidHeader = TRUE,
radioButtons(inputId = "distance",
label = "Which distance method do you want?", inline = TRUE,
choices = c("euclidean", "maximum", "manhattan", "canberra"),
selected = "euclidean")),
box(width = NULL, status ="primary",height = NULL,solidHeader = TRUE,
# https://support.minitab.com/en-us/minitab/18/help-and-how-to/modeling-statistics/multivariate/how-to/cluster-observations/methods-and-formulas/linkage-methods/
radioButtons(inputId = "clustering",
label = "Which clustering method do you want?", inline = TRUE,
choices = c("complete", "average", "mcquitty", "median", "centroid", "ward.D2"),
selected = "complete"))
), # end of changeCalcul=='yes'
box(width = NULL, status ="primary",height = NULL,solidHeader = TRUE,
radioButtons(inputId = "dendro",
label = "Do you want to display a column dendrogram?", inline = TRUE,
choices = c("no", "yes"),
selected = "no")),
box(width = NULL, status ="primary",height = NULL,solidHeader = TRUE,
uiOutput("nclustersUi")
),
box(width = NULL, status ="primary",height = NULL,solidHeader = TRUE,
radioButtons(inputId = "barcodes",
label = "Do you want to display a row barcodes?", inline = TRUE,
choices = c("no", "yes"),
selected = "no"))
) # end of graph options
) # end of conditionalPanel Heatmap
),
#), # end of left column
# Rigth column == Plot box
column(width=8, align="center",
###################
#### Heatmap ####
###################
conditionalPanel("input.graph_sampleSim=='Heatmap'",
tabBox(height="100%", width = "100%",
title = "",
id = "tabHeatmap",
tabPanel(id="tabFig",
title="Figure",
conditionalPanel("input.value.length==0",
imageOutput("heatmapEx", width="100%")),
conditionalPanel("input.value.length>0",
plotOutput(outputId="heatmap")),
conditionalPanel("input.value.length>0",
downloadButton("downloadImage_heatmap", "Plot"),
downloadButton("downloadTable_heatmap", "Matrix"))
),
tabPanel(id="tabInfo",
title="Details",
"Used distance: ",
conditionalPanel("input.value.length==0 ",
verbatimTextOutput("distanceEx")),
conditionalPanel("input.value.length>0 ",
verbatimTextOutput("distanceSelected")),
"Used clustering: ",
conditionalPanel("input.value.length==0 ",
verbatimTextOutput("clusteringEx")),
conditionalPanel("input.value.length>0 ",
verbatimTextOutput("clusteringSelected")))
) # end of tabBox
), # end of conditionalPanel heatmap
#######################
#### Correlogram ####
#######################
conditionalPanel("input.graph_sampleSim=='Correlogram'",
box(width = NULL, title="Graph options", status ="primary",solidHeader = TRUE,
box(width = NULL, status ="primary",height = NULL,solidHeader = TRUE,
radioButtons(inputId = "correlation",
label = "Choose your correlation method :", inline = TRUE,
choices = c("spearman", "pearson"),
selected = "pearson"))),
box(align="center", width = "100%", height = "100%",
#uiOutput("CloneSizeUI"),
conditionalPanel("input.value.length==0 ",
imageOutput("correloEx")),
conditionalPanel("input.value.length>0 ",
plotOutput(outputId="correlo"),
downloadButton("downloadImage_correlo", "Plot"),
downloadButton("downloadTable_correlo", "Matrix"))
)
) # end of condit panel Correlogram
)# end of right column
) # end of big box
) # end of fluidrow
), # end of tabItem sample_similaritiesMenu
#°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°
#####################
#### Clone size ###
#####################
tabItem(tabName = "clone_sizeMenu",
# Row of 2 big columns
fluidRow(
box(status = "primary", solidHeader = FALSE, width = "100%",
# Left column == questions box
column(width=4,
box(width = NULL, status ="primary",height = NULL,solidHeader = TRUE,
radioButtons(inputId = "graphType2",
label = "Select the type of graph:", inline = FALSE,
selected = "None",
choices = c("None", "Cumulative diagram", "Frequency distribution"))
),
conditionalPanel("input.graphType2!='None'",
box(width = NULL, title="Sample selections", status ="primary",solidHeader = TRUE,
box(width = NULL, status ="primary",solidHeader = TRUE,
pickerInput(inputId = "organismSampleCS",
label = "Which individual(s) do you want to display ?",
choices = NULL,
multiple = TRUE,
options = pickerOptions(actionsBox = TRUE,
title = "Individuals",
liveSearch = TRUE,
liveSearchStyle = "contains"))
),
box(width = NULL, status ="primary",height = 200,solidHeader = TRUE,
pickerInput(inputId = "variableCS",
label = "Which variable(s) do you want to display ?",
choices = NULL,
multiple = TRUE,
options = pickerOptions(actionsBox = TRUE,
title = "Variables",
liveSearch = TRUE,
liveSearchStyle = "contains")),
pickerInput(inputId = "valueCS",
label= "Select the value(s) take by variable(s):",
multiple = TRUE,
choices = NULL,
options = pickerOptions(actionsBox = TRUE,
title = "Values",
liveSearch = TRUE,
liveSearchStyle = "contains"))
)), # end of sample selection
box(width = NULL, title="Graph option", status ="primary",solidHeader = TRUE,
conditionalPanel("input.graphType2=='Frequency distribution'",
box(width = NULL, status ="primary",solidHeader = TRUE,
radioButtons(inputId = "yCS",
label= "Select the type of diagram:",
choices = c("Density curve", "Histogarm"),
selected = "Density curve",
inline = FALSE))
),
box(width = NULL, status ="primary",solidHeader = TRUE,
radioButtons(inputId = "doColor",
label= "Do you want to add colors :",
choices = c("no", "yes"),
selected = "no",
inline = FALSE),
conditionalPanel("input.doColor=='yes'",
pickerInput(inputId = "colorCS",
label= "Select the variable for the color:",
multiple = FALSE,
choices = NULL,
options = pickerOptions(actionsBox = FALSE,
title = "Color",
liveSearch = TRUE,
liveSearchStyle = "contains"))
)
),
# only freq
conditionalPanel("input.graphType2=='Frequency distribution'",
box(width = NULL, status ="primary",solidHeader = TRUE,
sliderInput("nbins", label = "Select a number of bins", min = 0,
max = 100, value = 5))
),
# only cum
conditionalPanel("input.graphType2=='Cumulative diagram'",
box(width = NULL, status ="primary",solidHeader = TRUE,
radioButtons(inputId ="xProportion",
label = "Convert x axis in percentage :",
choices = c("no", "yes"),
selected = "no",
inline = FALSE))
)
) # end of graph option
)
), #end of left box
column(width=8, align="center",
box(align="center", width = "100%", height = "100%",
## Clone Size ##
#°°°°°°°°°°°°°°°°°°°°°°°°#
#uiOutput("CloneSizeUI"),
conditionalPanel("input.graphType2=='Cumulative diagram' && input.valueCS.length==0 ",
imageOutput("cumulativeDiagramEx")),
conditionalPanel("input.graphType2=='Cumulative diagram' && input.valueCS.length>0 ",
plotOutput(outputId="cumulativeDiagram"),
downloadButton("downloadImage_cumDiag", "Plot"),
downloadButton("downloadTable_cumDiag", "Matrix")
),
conditionalPanel("input.graphType2=='Frequency distribution' && input.valueCS.length==0",
imageOutput("nonCumulativeHistEx")),
conditionalPanel("input.graphType2=='Frequency distribution' && input.valueCS.length>0 ",
plotOutput(outputId="nonCumulativeHist"),
downloadButton("downloadImage_nonCumHist", "Plot"),
downloadButton("downloadTable_nonCumHist", "Matrix")
)
) # end of right box
) # end of right column
) # end of big box
) # end of fluidrow
), # end of tabItem clone size
#°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°
##########################
#### Barcode sharing ###
#########################
tabItem(tabName = "barcode_sharingMenu",
# Row of 2 big columns
fluidRow(
box(status = "primary", solidHeader = FALSE, width = "100%",
# Left column == questions box
column(width=4,
box(width = NULL, status ="primary",height = NULL,solidHeader = TRUE,
radioButtons(inputId = "graphType1",
label = "Select the type of graph:", inline = FALSE,
selected = "None",
choices = c("None", "Dotplot", "Ternary plot"))
),
conditionalPanel("input.graphType1!='None'",
box(width = NULL, title="Sample selections", status ="primary",solidHeader = TRUE,
box(width = NULL, status ="primary",solidHeader = TRUE,
pickerInput(inputId = "organismSampleSB",
label = "Which individual(s) do you want to display ?",
choices = NULL,
multiple = TRUE,
options = pickerOptions(actionsBox = TRUE,
title = "Individuals",
liveSearch = TRUE,
liveSearchStyle = "contains"))
),
conditionalPanel("input.graphType1=='Dotplot'",
box(width = NULL,title="x axis", status ="primary",solidHeader = TRUE,
pickerInput(inputId = "x_var",
label = "Select x variable(s):",
choices = NULL,
multiple = TRUE,
options = pickerOptions(actionsBox = TRUE,
title = "Variables",
liveSearch = TRUE,
liveSearchStyle = "contains")),
pickerInput(inputId = "x_val",
label = "Select x value(s) to display:",
choices = NULL,
multiple = TRUE,
options = pickerOptions(actionsBox = TRUE,
title = "Values",
liveSearch = TRUE,
liveSearchStyle = "contains"))
),
box(width = NULL,title="y axis", status ="primary",solidHeader = TRUE,
pickerInput(inputId = "y_var",
label = "Select y variable(s):",
choices = NULL,
multiple = TRUE,
options = pickerOptions(actionsBox = TRUE,
title = "Variables",
liveSearch = TRUE,
liveSearchStyle = "contains")),
pickerInput(inputId = "y_val",
label = "Select y value(s) to display:",
choices = NULL,
multiple = TRUE,
options = pickerOptions(actionsBox = TRUE,
title = "Values",
liveSearch = TRUE,
liveSearchStyle = "contains"))
)), # end of conditionalPanel Dotplot
conditionalPanel("input.graphType1=='Ternary plot'",
box(width = NULL,title="Value1", status ="primary",solidHeader = TRUE,
pickerInput(inputId = "top_var",
label= "Select variable(s):",
multiple = TRUE,
choices = NULL,
options = pickerOptions(actionsBox = TRUE,
title = "Variables",
liveSearch = TRUE,
liveSearchStyle = "contains")),
pickerInput(inputId = "top_val",
label= "Select values(s) to display (left axis):",
multiple = TRUE,
choices = NULL,
options = pickerOptions(actionsBox = TRUE,
title = "Values",
liveSearch = TRUE,
liveSearchStyle = "contains"))
),
box(width = NULL,title="Value2", status ="primary",solidHeader = TRUE,
pickerInput(inputId = "right_var",
label= "Select variable(s):",
multiple = TRUE,
choices = NULL,
options = pickerOptions(actionsBox = TRUE,
title = "Variables",
liveSearch = TRUE,
liveSearchStyle = "contains")),
pickerInput(inputId = "right_val",
label= "Select values(s) to display (right axis):",
multiple = TRUE,
choices = NULL,
options = pickerOptions(actionsBox = TRUE,
title = "Values",
liveSearch = TRUE,
liveSearchStyle = "contains"))
),
box(width = NULL,title="Value3", status ="primary",solidHeader = TRUE,
pickerInput(inputId = "left_var",
label= "Select variable(s):",
multiple = TRUE,
choices = NULL,
options = pickerOptions(actionsBox = TRUE,
title = "Variables",
liveSearch = TRUE,
liveSearchStyle = "contains")),
pickerInput(inputId = "left_val",
label= "Select values(s) to display (bottom axis):",
multiple = TRUE,
choices = NULL,
options = pickerOptions(actionsBox = TRUE,
title = "Values",
liveSearch = TRUE,
liveSearchStyle = "contains"))
)
) # end of conditional panel Ternary
), # end of sample selection
box(width = NULL, title="Graph options", status ="primary",solidHeader = TRUE,
conditionalPanel("input.graphType1=='Dotplot'",
box(width = NULL, status ="primary",height = NULL,solidHeader = TRUE,
radioButtons(inputId = "SBtransformation",
label = "Which transformation do you want to apply? ", inline = TRUE,
selected = "arcsin",
choices = c("arcsin", "log10(x+1)", "none"))
)
),
conditionalPanel("input.graphType1=='Dotplot'",
box(width = NULL, status ="primary",height = NULL,solidHeader = TRUE,
radioButtons(inputId = "filledPlotSB",
label = "Do you want to color dots?", inline = TRUE,
selected = "no",
choices = c("no", "yes")),
conditionalPanel("input.filledPlotSB=='yes'" ,
pickerInput(inputId = "colorSB",
label= "Select the variable to color:",
multiple = FALSE,
choices = NULL,
options = pickerOptions(actionsBox = TRUE,
title = "Color",
liveSearch = FALSE))
)
)
),
conditionalPanel("input.graphType1=='Ternary plot'" ,
radioButtons(inputId = "colorSB_ternary",
label = "Do you want to color dots according individuals ?", inline = TRUE,
selected = "no",
choices = c("no", "yes")))
) # end of graph options
) #end of conditionalPanel not None
), # end of left column
column(width=8, align="center",
box(align="center", width = "100%", height = "100%",
conditionalPanel("input.graphType1=='Dotplot' && (input.x_val.length==0 || input.y_val.length==0) ",
imageOutput("dotplotEx")),
conditionalPanel("input.graphType1=='Dotplot' && input.x_val.length>0 && input.y_val.length>0 ",
# dotplot
plotOutput(outputId="dotplot"),
downloadButton("downloadImage_dotplot", "Plot"),
downloadButton("downloadTable_dotplot", "Matrix"),
# piechart plot
plotOutput(outputId="piechart"),
downloadButton("downloadImage_piechart", "Plot"),
downloadButton("downloadTable_piechart", "Matrix")),
conditionalPanel("input.graphType1=='Ternary plot' && (input.top_val.length==0 || input.left_val.length==0 || input.right_val.length==0)",
imageOutput("ternaryPlotEx")),
conditionalPanel("input.graphType1=='Ternary plot' && input.top_val.length>0 && input.left_val.length>0 && input.right_val.length>0",
plotOutput(outputId="ternaryPlot"),
downloadButton("downloadImage_ternary", "Plot"),
downloadButton("downloadTable_ternary", "Matrix"))
) # end of right box
) # end of right column
) # end of big box
) # end of fluidrow
), # end of tabItem barcode sharing
#°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°
####################
#### Diversity ###
####################
tabItem(tabName = "diversityMenu",
# Row of 2 big columns
fluidRow(
box(status = "primary", solidHeader = FALSE, width = "100%",
# Left column == questions box
column(width=4,
box(width = NULL, title="Sample selections", status ="primary",solidHeader = TRUE,
# changer pour le dotplot, proposer uniquement un seul choix pour la variable
box(width = NULL, status ="primary",solidHeader = TRUE,
pickerInput(inputId = "organismSample_notPooled",
label = "Select individual(s): ",
choices = NULL,
multiple = TRUE,
options = pickerOptions(actionsBox = TRUE,
title = "Individuals",
liveSearch = TRUE,
liveSearchStyle = "contains"))
),
box(width = NULL, status ="primary",solidHeader = TRUE,
pickerInput(inputId = "variable_notPooled",
label = "Select x axis variable(s):",
choices = NULL,
multiple = TRUE,
options = pickerOptions(actionsBox = TRUE,
title = "Variables",
liveSearch = TRUE,
liveSearchStyle = "contains")),
pickerInput(inputId = "value_notPooled",
label= "Select value(s) take by x axis variable(s):",
multiple = TRUE,
choices = NULL,
options = pickerOptions(actionsBox = TRUE,
title = "Values",
liveSearch = TRUE,
liveSearchStyle = "contains"))
),
box(width = NULL, status ="primary",solidHeader = TRUE,
radioButtons(inputId = "yBoxplot",
label = "What do you want in y axis ?", inline = TRUE,
selected = "Number of barcodes",
choices = c("Number of barcodes", "Shannon index", "Simpson index"))
)
), # end of box Sample selection
box(width = NULL, title="Graph options", status ="primary",solidHeader = TRUE,
box(width = NULL, status ="primary",solidHeader = TRUE,
radioButtons(inputId = "boxplotCondition",
label = "Do you want to color your plot ?", inline = TRUE,
selected = "no",
choices = c("no", "yes")),
conditionalPanel("input.boxplotCondition=='yes'",
pickerInput(inputId = "boxplotColor_var",
label= "Select a variable: ",
multiple = FALSE,
choices = NULL,
options = pickerOptions(actionsBox = FALSE,
title = "Variable",
liveSearch = FALSE))
)),
box(width = NULL, status ="primary",solidHeader = TRUE,
radioButtons(inputId = "boxplotDot",
label = "Do you want to display dots?", inline = TRUE,
selected = "no",
choices = c("no", "yes"))
)
) # end of Graph options
), # end of left column
column(width=8, align="center",
box(align="center", width = "100%", height = "100%",
conditionalPanel("input.value_notPooled.length<1",
imageOutput("boxplotEx")),
conditionalPanel("input.value_notPooled.length>=1",
plotOutput(outputId="boxplot"),
downloadButton("downloadImage_boxplot", "Plot"),
downloadButton("downloadTable_boxplot", "Matrix"))
) # end of right box
) # end of right column
) # end of big box
) # end of fluidrow
), # end of tabItem diversityMenu
#°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°
#########################
#### Categorisation ###
#########################
tabItem(tabName = "categorisationMenu",
# Row of 2 big columns
fluidRow(
box(status = "primary", solidHeader = FALSE, width = "100%",
# Left column == questions box
column(width=4,
box(width = NULL, status ="primary",height = NULL,solidHeader = TRUE,
radioButtons(inputId = "CatGraph",
label = "Select the analysis:", inline = FALSE,
selected = "None",
choices = c("None", "Category analysis", "Bias analysis"))
),
conditionalPanel("input.CatGraph!='None'",
box(width = NULL, status ="primary",solidHeader = TRUE, title="Sample selections",
pickerInput(inputId = "organismCat",
label = "Select individual(s):",
choices = NULL,
multiple = TRUE,
options = pickerOptions(actionsBox = TRUE,
title = "Individuals",
liveSearch = TRUE,
liveSearchStyle = "contains")),
pickerInput(inputId = "catVar",
label = "Select the variable used for cell types:",
choices = NULL,
multiple = FALSE,
options = pickerOptions(actionsBox = TRUE,
title = "Categorgy",
liveSearch = TRUE,
liveSearchStyle = "contains")),
conditionalPanel("input.catVar!=''",
pickerInput(inputId = "catVal",
label = "Select its values:",
choices = NULL,
multiple = TRUE,
options = pickerOptions(actionsBox = TRUE,
liveSearch = TRUE,
liveSearchStyle = "contains"))),
conditionalPanel("input.catVar!='' && input.catVal.length>1 && input.CatGraph=='Bias analysis'",
pickerInput(inputId = "yBias",
label = "Select one cell type:",
choices = NULL,
multiple = FALSE,
options = pickerOptions(actionsBox = TRUE,
liveSearch = TRUE,
liveSearchStyle = "contains")))
), # end of Sample selections
box(width = NULL, status ="primary",solidHeader = TRUE,title="Graph option",
conditionalPanel("input.CatGraph=='Category analysis'",
box(width = NULL, status ="primary",solidHeader = TRUE,title="Threshold value",
sliderInput("slider", label = "Select the threshold used for categorization:", min = 0,
max = 100, value = 20))),
radioButtons(inputId = "condition",
label = "Do you want to add a condition (e.g: treatment, organ, etc.) ? ", inline = TRUE,
selected = "no",
choices = c("no","yes")),
conditionalPanel("input.condition=='yes' && input.catVar!=''",
pickerInput(inputId = "conditionVal",
label = "Select your condition value:",
choices = NULL,
multiple = FALSE,
options = pickerOptions(actionsBox = TRUE,
title = "Condition",
liveSearch = TRUE,
liveSearchStyle = "contains")))
) # end of box Graph opt
) # end of conditional None
), # end of left column
column(width=8, align="center",
box(align="center", width = "100%", height = "100%",
conditionalPanel("input.CatGraph=='Category analysis'",
conditionalPanel("input.catVal.length<=1 && input.organismCat.length==0",
imageOutput("contrib2"),
imageOutput("contrib1")
)),
conditionalPanel("input.catVal.length>1 && input.organismCat.length>0 && input.CatGraph=='Category analysis'",
# first plot
withLoader(plotOutput(outputId="bargraphCat_counts"), type = "html", loader = "dnaspin"),
downloadButton("downloadImage_counts", "Plot"),
downloadButton("downloadTable_counts", "Matrix"),
# second plot
plotOutput(outputId="bargraphCat_percent"),
downloadButton("downloadImage_percent", "Plot"),
downloadButton("downloadTable_percent", "Matrix")
),
# print and export bias analysis graphs and matrices
conditionalPanel("input.catVal.length>1 && input.organismCat.length>0 && input.CatGraph=='Bias analysis'",
# first plot
withLoader(plotOutput(outputId="biasPerType"), type = "html", loader = "dnaspin"),
downloadButton("downloadImage_biasType", "Plot"),
downloadButton("downloadTable_biasType", "Matrix"),
# second plot
plotOutput(outputId="biasPerCat"),
downloadButton("downloadImage_biasCat", "Plot"),
downloadButton("downloadTable_biasCat", "Matrix")
)
) # end of right box
) # end of right column
) # end of big box
) # end of fluidrow
) # end of tabItem categorisationMenu
)# end of TabItems
)# end of fluidPage
)# end dashboardBody
)# end dashboardPage
}
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