R/mod_upload.R
In martaint/InterCellar: InterCellar: an R-Shiny app for interactive analysis and exploration of cell-cell communication in single-cell transcriptomics
Defines functions
mod_upload_server
mod_upload_ui
#' upload UI Function
#'
#' @description A shiny Module.
#'
#' @param id,input,output,session Internal parameters for {shiny}.
#'
#' @noRd
#'
#' @importFrom shiny NS tagList fluidRow column selectInput conditionalPanel
#' textOutput tabPanel
#' @importFrom shinyFiles shinyDirButton shinyDirChoose getVolumes parseDirPath
#' @importFrom shinydashboard tabBox
#' @importFrom fs path_home
mod_upload_ui <- function(id){
ns <- NS(id)
supported.tools.list <- list("CellPhoneDB v2" = "cpdbv2",
"CellChat" = "cellchat",
"ICELLNET" = "icellnet",
"SingleCellSignalR" = "scsignalR"
)
text.cpdb <- "Please select the output folder generated by CPDB (v2). When the
statistical analysis was run, this folder contains 4 .txt files
(<em>deconvoluted</em>, <em>means</em>, <em>pvalues</em> and
<em>significant_means</em>). In this case, InterCellar will use results stored
in <em>significant_means</em> for further analyses. If no statistical analysis
was run, InterCellar will rely on <em>means</em>."
text.scsignalR <- "Please select the output folder generated by
SingleCellSignalR. This is by default named <em>cell-signaling</em> and
contains a collection of .txt files, one for each clusters pair considered."
text.cellchat <- "InterCellar expects a dataframe consisting of inferred cell-cell
communications at the level of ligand-receptor interactions. This can be obtained
by running CellChat's function <em>subsetCommunication (with param slot.name = 'net')</em>.
We recommend saving this dataframe as a .csv file (quote = FALSE), but .tsv and .xlsx files are also supported."
text.icellnet <- "InterCellar accepts a dataframe obtained by running ICELLNET's function <em>icellnet.score</em>. Please
specifiy the direction of communication ('out' or 'in') and give a name to the <em>central cell</em>. The dataframe should
be saved as a .csv file (with row.names = TRUE)."
tagList(
fluidRow(
column(width = 6,
h2("Upload cell-cell interactions")),
),
fluidRow(
box(width = 12,
title = h3("Analysis setup"),
column(width = 6,
h4("Please select an existing local folder where InterCellar will save all results of your analysis."),
),
column(width = 6,
shinyFiles::shinyDirButton(ns("out_folder"),
"Select folder",
"Please select a folder",
icon = icon("folder")),
verbatimTextOutput(ns("path_out_folder"))
)
)
),
tabBox(
width = NULL,
tabPanel(h4("From supported tools"),
fluidRow(
box(width = 12,
title = "CCI data #1",
status = "primary",
collapsible = TRUE,
solidHeader = TRUE,
column(6,
textInput(ns("db1_name"),
label = h4("CCI data ID"),
placeholder = "my_CCI_data1"),
textInput(ns("db1_out_folder"),
label = h4("Output folder tag"),
value = NULL,
placeholder = "my_out_folder1")
),
column(6,
selectInput(ns("select_input_tool1"),
label = h4("Select tool:"),
choices = supported.tools.list,
multiple = FALSE),
# Conditional panels
conditionalPanel(
condition = "input.select_input_tool1 == 'cpdbv2'",
ns = ns,
p(div(HTML(text.cpdb)))
),
conditionalPanel(
condition = "input.select_input_tool1 == 'scsignalR'",
ns = ns,
p(div(HTML(text.scsignalR)))
),
conditionalPanel(
condition = "input.select_input_tool1 == 'cellchat'",
ns = ns,
p(div(HTML(text.cellchat)))
),
conditionalPanel(
condition = "input.select_input_tool1 == 'icellnet'",
ns = ns,
p(div(HTML(text.icellnet)))
),
conditionalPanel(
condition = "input.select_input_tool1 == 'cpdbv2' | input.select_input_tool1 == 'scsignalR'",
ns = ns,
shinyFiles::shinyDirButton(ns("directory1"),
"Select folder",
"Please select a folder"),
verbatimTextOutput(ns("selected_folder1"))
),
conditionalPanel(
condition = "input.select_input_tool1 == 'cellchat' | input.select_input_tool1 == 'icellnet'",
ns = ns,
fileInput(ns("input_file1"),
"Choose Input File (.csv/.tsv/.xlsx)",
multiple = FALSE,
accept = c(".csv", ".tsv", ".xlsx"))
),
conditionalPanel(
condition = "input.select_input_tool1 == 'icellnet'",
ns = ns,
radioButtons(ns("icellnet_dir_1"),
label = "Select direction:",
choices = list("out", "in"),
inline = TRUE),
textInput(ns("icellnet_CC_1"),
label = "Central cell name",
value = NULL,
placeholder = "B cells")
)
##
),
fluidRow(column(width = 1, offset = 11,
actionButton(ns("input_file_button1"),
label = h4("GO!"),
class = "btn-primary")
))
)),
fluidRow(
box(width = 12,
title = "CCI data #2",
status = "warning",
collapsible = TRUE,
collapsed = TRUE,
solidHeader = TRUE,
column(6,
textInput(ns("db2_name"),
label = h4("CCI data ID"),
placeholder = "my_CCI_data2"),
textInput(ns("db2_out_folder"),
label = h4("Output folder tag"),
value = NULL,
placeholder = "my_out_folder2")
),
column(6,
selectInput(ns("select_input_tool2"),
label = h4("Select tool:"),
choices = supported.tools.list,
multiple = FALSE),
# Conditional panels
conditionalPanel(
condition = "input.select_input_tool2 == 'cpdbv2'",
ns = ns,
p(div(HTML(text.cpdb)))
),
conditionalPanel(
condition = "input.select_input_tool2 == 'scsignalR'",
ns = ns,
p(div(HTML(text.scsignalR)))
),
conditionalPanel(
condition = "input.select_input_tool2 == 'cellchat'",
ns = ns,
p(div(HTML(text.cellchat)))
),
conditionalPanel(
condition = "input.select_input_tool2 == 'icellnet'",
ns = ns,
p(div(HTML(text.icellnet)))
),
conditionalPanel(
condition = "input.select_input_tool2 == 'cpdbv2' | input.select_input_tool2 == 'scsignalR'",
ns = ns,
shinyFiles::shinyDirButton(ns("directory2"),
"Select folder",
"Please select a folder"),
verbatimTextOutput(ns("selected_folder2"))
),
conditionalPanel(
condition = "input.select_input_tool2 == 'cellchat' | input.select_input_tool2 == 'icellnet'",
ns = ns,
fileInput(ns("input_file2"),
"Choose Input File (.csv/.tsv/.xlsx)",
multiple = FALSE,
accept = c(".csv", ".tsv", ".xlsx"))
),
conditionalPanel(
condition = "input.select_input_tool2 == 'icellnet'",
ns = ns,
radioButtons(ns("icellnet_dir_2"),
label = "Select direction:",
choices = list("out", "in"),
inline = TRUE),
textInput(ns("icellnet_CC_2"),
label = "Central cell name",
value = NULL,
placeholder = "B cells")
)
##
),
fluidRow(column(width = 1, offset = 11,
actionButton(ns("input_file_button2"),
label = h4("GO!"),
class = "btn-warning")
))
)),
fluidRow(
box(width = 12,
title = "CCI data #3",
status = "danger",
collapsible = TRUE,
collapsed = TRUE,
solidHeader = TRUE,
column(6,
textInput(ns("db3_name"),
label = h4("CCI data ID"),
placeholder = "my_CCI_data3"),
textInput(ns("db3_out_folder"),
label = h4("Output folder tag"),
value = NULL,
placeholder = "my_out_folder3")
),
column(6,
selectInput(ns("select_input_tool3"),
label = h4("Select tool:"),
choices = supported.tools.list,
multiple = FALSE),
# Conditional panels
conditionalPanel(
condition = "input.select_input_tool3 == 'cpdbv2'",
ns = ns,
p(div(HTML(text.cpdb)))
),
conditionalPanel(
condition = "input.select_input_tool3 == 'scsignalR'",
ns = ns,
p(div(HTML(text.scsignalR)))
),
conditionalPanel(
condition = "input.select_input_tool3 == 'cellchat'",
ns = ns,
p(div(HTML(text.cellchat)))
),
conditionalPanel(
condition = "input.select_input_tool3 == 'icellnet'",
ns = ns,
p(div(HTML(text.icellnet)))
),
conditionalPanel(
condition = "input.select_input_tool3 == 'cpdbv2' | input.select_input_tool3 == 'scsignalR'",
ns = ns,
shinyFiles::shinyDirButton(ns("directory3"),
"Select folder",
"Please select a folder"),
verbatimTextOutput(ns("selected_folder3"))
),
conditionalPanel(
condition = "input.select_input_tool3 == 'cellchat' | input.select_input_tool3 == 'icellnet'",
ns = ns,
fileInput(ns("input_file3"),
"Choose Input File (.csv/.tsv/.xlsx)",
multiple = FALSE,
accept = c(".csv", ".tsv", ".xlsx"))
),
conditionalPanel(
condition = "input.select_input_tool3 == 'icellnet'",
ns = ns,
radioButtons(ns("icellnet_dir_3"),
label = "Select direction:",
choices = list("out", "in"),
inline = TRUE),
textInput(ns("icellnet_CC_3"),
label = "Central cell name",
value = NULL,
placeholder = "B cells")
)
##
),
fluidRow(column(width = 1, offset = 11,
actionButton(ns("input_file_button3"),
label = h4("GO!"),
class = "btn-danger")
))
))
), #tabpanel
tabPanel(h4("From custom analysis"),
mod_upload_custom_ui("upload_custom_ui_1")
)
)#tabbox
)
}
#' upload Server Function
#'
#' @importFrom shinyalert shinyalert
#' @noRd
mod_upload_server <- function(id) {
moduleServer(id, function(input, output, session) {
rv <- reactiveValues(data = list(db1 = NULL,
db2 = NULL,
db3 = NULL),
db_names = list(db1 = NULL,
db2 = NULL,
db3 = NULL),
output_folders_path = list(db1 = NULL,
db2 = NULL,
db3 = NULL),
output_folder = NULL,
output_tags = list(db1 = NULL,
db2 = NULL,
db3 = NULL))
### For supported tools requiring folders
volumes <- c(Home = fs::path_home(), getVolumes()())
## CCI data 1
shinyDirChoose(input, "directory1", roots = volumes, session = session,
restrictions = system.file(package = "base"))
input_folder1 <- reactive({
req(input$directory1)
parseDirPath(volumes, input$directory1)
})
output$selected_folder1 <- renderText({
input_folder1()
})
## CCI data 2
shinyDirChoose(input, "directory2", roots = volumes, session = session,
restrictions = system.file(package = "base"))
input_folder2 <- reactive({
req(input$directory2)
parseDirPath(volumes, input$directory2)
})
output$selected_folder2 <- renderText({
input_folder2()
})
## CCI data 3
shinyDirChoose(input, "directory3", roots = volumes, session = session,
restrictions = system.file(package = "base"))
input_folder3 <- reactive({
req(input$directory3)
parseDirPath(volumes, input$directory3)
})
output$selected_folder3 <- renderText({
input_folder3()
})
### Output folder
shinyDirChoose(input, "out_folder", roots = volumes, session = session,
restrictions = system.file(package = "base"))
output_folder <- reactive({
#req(input$out_folder)
parseDirPath(volumes, input$out_folder)
})
output$path_out_folder <- renderText({
output_folder()
})
observeEvent(output_folder(), {
rv$output_folder <- output_folder()
})
### CCI data 1
### Read input and construct datatable
observeEvent(input$input_file_button1, {
if(input$db1_name == ""){
shinyalert(text = "Please specify an ID for your CCI data #1!", type = "error",
showCancelButton = FALSE)
}
if(input$db1_out_folder == ""){
shinyalert(text = "Please specify an output folder tag for your CCI data #1!", type = "error",
showCancelButton = FALSE)
}
if(identical(output_folder(), character(0))){
shinyalert(text = "Please select an output folder!",
type = "error",
showCancelButton = FALSE)
}
req(output_folder())
req(input$db1_name, input$db1_out_folder)
#check that tags are not repeated
tags <- c(input$db1_out_folder, input$db2_out_folder, input$db3_out_folder)
tags <- tags[!(tags == "")]
if(any(duplicated(tags))){
shinyalert(text = "It looks like tags for output folders are not unique! Please re-upload your data after changing repeated tags
to avoid overwriting results!",
type = "error",
showCancelButton = FALSE)
} else {
# create directory with tags
dir.create(file.path(output_folder(), paste0("InterCellar_results_", input$db1_out_folder)))
shinyalert(text = paste0("Directory created: ", file.path(output_folder(), paste0("InterCellar_results_", input$db1_out_folder))),
type = "success",
showCancelButton = FALSE,
timer = 4000)
rv$output_folders_path$db1 <- file.path(output_folder(), paste0("InterCellar_results_", input$db1_out_folder))
}
rv$db_names$db1 <- as.character(input$db1_name)
rv$output_tags$db1 <- input$db1_out_folder
if(input$select_input_tool1 == 'cpdbv2'){
req(input_folder1())
files <- list.files(input_folder1())
if("means.txt" %in% files){
rv$data$db1 <- read.CPDBv2(folder = input_folder1())
shinyalert(text = "Your data was successfully loaded and preprocessed!",
type = "success",
showCancelButton = FALSE)
} else {
shinyalert(text = "The selected folder does not contain CPDB output files!
Please select the correct folder.",
type = "error",
showCancelButton = FALSE)
}
}
else if(input$select_input_tool1 == 'scsignalR'){
req(input_folder1())
files <- list.files(input_folder1())
if(all(grep("LR_interactions", files))){
rv$data$db1 <- read.SCsignalR(folder = input_folder1())
shinyalert(text = "Your data was successfully loaded and preprocessed!",
type = "success",
showCancelButton = FALSE)
} else{
shinyalert(text = "The selected folder does not contain
SingleCellSignalR output files!
Please select the correct folder.",
type = "error",
showCancelButton = FALSE)
}
} else if(input$select_input_tool1 == 'cellchat'){
file <- input$input_file1
req(file)
ext <- tools::file_ext(file$datapath)
validate(need(ext %in% c("csv", "tsv", "xlsx"), "Please choose a file
with the required extension (.csv/.tsv/.xlsx)."))
switch (ext,
csv = {tryCatch({
tab <- read.csv(file$datapath, header = TRUE)
if("X" %in% colnames(tab)){
tab <- tab[, !colnames(tab) == "X"]
}
},
error = function(e) {
# return a safeError if a parsing error occurs
stop(safeError("Error reading input file"))
}
)},
tsv = {tryCatch({
tab <- read.table(file$datapath, sep = "\t",
header = TRUE)
},
error = function(e) {
# return a safeError if a parsing error occurs
stop(safeError("Error reading input file"))
}
)},
xlsx = {tryCatch({
tab <- read_excel(file$datapath, col_names = TRUE)
},
error = function(e) {
# return a safeError if a parsing error occurs
stop(safeError("Error reading input file"))
}
)}
)
# Checks on required columns
req.columns <- c("source", "target", "ligand", "receptor", "prob", "pval",
"interaction_name", "interaction_name_2", "pathway_name",
"annotation", "evidence")
if(!all(req.columns %in% colnames(tab))){
missing.col <- req.columns[!(req.columns %in% colnames(tab))]
shinyalert(text = paste("Looks like these required columns are missing:",
paste(missing.col, collapse = " "), sep = " "),
type = "error",
showCancelButton = FALSE)
} else {
rv$data$db1 <- suppressWarnings(read.cellchat(tab))
shinyalert(text = "Your data was successfully loaded and preprocessed!",
type = "success",
showCancelButton = FALSE)
}
} else if(input$select_input_tool1 == 'icellnet'){
file <- input$input_file1
req(file)
ext <- tools::file_ext(file$datapath)
validate(need(ext %in% c("csv"), "Please choose a file
with the required extension (.csv)."))
switch (ext,
csv = {tryCatch({
tab <- read.csv(file$datapath)
},
error = function(e) {
# return a safeError if a parsing error occurs
stop(safeError("Error reading input file"))
}
)}
)
validate(need(input$icellnet_CC_1, "Please give a name to the central cell!"))
rv$data$db1 <- suppressWarnings(read.icellnet(tab, input$icellnet_CC_1, input$icellnet_dir_1))
shinyalert(text = "Your data was successfully loaded and preprocessed!",
type = "success",
showCancelButton = FALSE)
}
})
### CCI data 2
### Read input and construct datatable
observeEvent(input$input_file_button2, {
if(input$db2_name == ""){
shinyalert(text = "Please specify an ID for your CCI data #2!", type = "error",
showCancelButton = FALSE)
}
if(input$db2_out_folder == ""){
shinyalert(text = "Please specify an output folder tag for your CCI data #2!", type = "error",
showCancelButton = FALSE)
}
if(identical(output_folder(), character(0))){
shinyalert(text = "Please select an output folder!",
type = "error",
showCancelButton = FALSE)
}
req(output_folder())
req(input$db2_name, input$db2_out_folder)
#check that tags are not repeated
tags <- c(input$db1_out_folder, input$db2_out_folder, input$db3_out_folder)
tags <- tags[!(tags == "")]
if(any(duplicated(tags))){
shinyalert(text = "It looks like tags for output folders are not unique! Please re-upload your data after changing repeated tags
to avoid overwriting results!",
type = "error",
showCancelButton = FALSE)
} else {
# create directory with tags
dir.create(file.path(output_folder(), paste0("InterCellar_results_", input$db2_out_folder)))
shinyalert(text = paste0("Directory created: ", file.path(output_folder(), paste0("InterCellar_results_", input$db2_out_folder))),
type = "success",
showCancelButton = FALSE,
timer = 4000)
rv$output_folders_path$db2 <- file.path(output_folder(), paste0("InterCellar_results_", input$db2_out_folder))
}
rv$db_names$db2 <- as.character(input$db2_name)
rv$output_tags$db2 <- input$db2_out_folder
if(input$select_input_tool2 == 'cpdbv2'){
req(input_folder2())
files <- list.files(input_folder2())
if("means.txt" %in% files){
rv$data$db2 <- read.CPDBv2(folder = input_folder2())
shinyalert(text = "Your data was successfully loaded and preprocessed!",
type = "success",
showCancelButton = FALSE)
} else {
shinyalert(text = "The selected folder does not contain CPDB output files!
Please select the correct folder.",
type = "error",
showCancelButton = FALSE)
}
}
else if(input$select_input_tool2 == 'scsignalR'){
req(input_folder2())
files <- list.files(input_folder2())
if(all(grep("LR_interactions", files))){
rv$data$db2 <- read.SCsignalR(folder = input_folder2())
shinyalert(text = "Your data was successfully loaded and preprocessed!",
type = "success",
showCancelButton = FALSE)
} else{
shinyalert(text = "The selected folder does not contain
SingleCellSignalR output files!
Please select the correct folder.",
type = "error",
showCancelButton = FALSE)
}
} else if(input$select_input_tool2 == 'cellchat'){ # add here other file input tools
file <- input$input_file2
req(file)
ext <- tools::file_ext(file$datapath)
validate(need(ext %in% c("csv", "tsv", "xlsx"), "Please choose a file
with the required extension (.csv/.tsv/.xlsx)."))
switch (ext,
csv = {tryCatch({
tab <- read.csv(file$datapath, header = TRUE)
if("X" %in% colnames(tab)){
tab <- tab[, !colnames(tab) == "X"]
}
},
error = function(e) {
# return a safeError if a parsing error occurs
stop(safeError("Error reading input file"))
}
)},
tsv = {tryCatch({
tab <- read.table(file$datapath, sep = "\t",
header = TRUE)
},
error = function(e) {
# return a safeError if a parsing error occurs
stop(safeError("Error reading input file"))
}
)},
xlsx = {tryCatch({
tab <- read_excel(file$datapath, col_names = TRUE)
},
error = function(e) {
# return a safeError if a parsing error occurs
stop(safeError("Error reading input file"))
}
)}
)
# Checks on required columns
req.columns <- c("source", "target", "ligand", "receptor", "prob", "pval",
"interaction_name", "interaction_name_2", "pathway_name",
"annotation", "evidence")
if(!all(req.columns %in% colnames(tab))){
missing.col <- req.columns[!(req.columns %in% colnames(tab))]
shinyalert(text = paste("Looks like these required columns are missing:",
paste(missing.col, collapse = " "), sep = " "),
type = "error",
showCancelButton = FALSE)
} else {
rv$data$db2 <- suppressWarnings(read.cellchat(tab))
shinyalert(text = "Your data was successfully loaded and preprocessed!",
type = "success",
showCancelButton = FALSE)
}
} else if(input$select_input_tool2 == 'icellnet'){
file <- input$input_file2
req(file)
ext <- tools::file_ext(file$datapath)
validate(need(ext %in% c("csv"), "Please choose a file
with the required extension (.csv)."))
switch (ext,
csv = {tryCatch({
tab <- read.csv(file$datapath)
},
error = function(e) {
# return a safeError if a parsing error occurs
stop(safeError("Error reading input file"))
}
)}
)
validate(need(input$icellnet_CC_2, "Please give a name to the central cell!"))
rv$data$db2 <- suppressWarnings(read.icellnet(tab, input$icellnet_CC_2, input$icellnet_dir_2))
shinyalert(text = "Your data was successfully loaded and preprocessed!",
type = "success",
showCancelButton = FALSE)
}
})
### CCI data 3
### Read input and construct datatable
observeEvent(input$input_file_button3, {
if(input$db3_name == ""){
shinyalert(text = "Please specify an ID for your CCI data #3!", type = "error",
showCancelButton = FALSE)
}
if(input$db3_out_folder == ""){
shinyalert(text = "Please specify an output folder tag for your CCI data #3!", type = "error",
showCancelButton = FALSE)
}
if(identical(output_folder(), character(0))){
shinyalert(text = "Please select an output folder!",
type = "error",
showCancelButton = FALSE)
}
req(output_folder())
req(input$db3_name, input$db3_out_folder)
#check that tags are not repeated
tags <- c(input$db1_out_folder, input$db2_out_folder, input$db3_out_folder)
tags <- tags[!(tags == "")]
if(any(duplicated(tags))){
shinyalert(text = "It looks like tags for output folders are not unique! Please re-upload your data after changing repeated tags
to avoid overwriting results!",
type = "error",
showCancelButton = FALSE)
} else {
# create directory with tags
dir.create(file.path(output_folder(), paste0("InterCellar_results_", input$db3_out_folder)))
shinyalert(text = paste0("Directory created: ", file.path(output_folder(), paste0("InterCellar_results_", input$db3_out_folder))),
type = "success",
showCancelButton = FALSE,
timer = 4000)
rv$output_folders_path$db3 <- file.path(output_folder(), paste0("InterCellar_results_", input$db3_out_folder))
}
rv$db_names$db3 <- as.character(input$db3_name)
rv$output_tags$db3 <- input$db3_out_folder
if(input$select_input_tool3 == 'cpdbv2'){
req(input_folder3())
files <- list.files(input_folder3())
if("means.txt" %in% files){
rv$data$db3 <- read.CPDBv2(folder = input_folder3())
shinyalert(text = "Your data was successfully loaded and preprocessed!",
type = "success",
showCancelButton = FALSE)
} else {
shinyalert(text = "The selected folder does not contain CPDB output files!
Please select the correct folder.",
type = "error",
showCancelButton = FALSE)
}
}
else if(input$select_input_tool3 == 'scsignalR'){
req(input_folder3())
files <- list.files(input_folder3())
if(all(grep("LR_interactions", files))){
rv$data$db3 <- read.SCsignalR(folder = input_folder3())
shinyalert(text = "Your data was successfully loaded and preprocessed!",
type = "success",
showCancelButton = FALSE)
} else{
shinyalert(text = "The selected folder does not contain
SingleCellSignalR output files!
Please select the correct folder.",
type = "error",
showCancelButton = FALSE)
}
} else if(input$select_input_tool3 == 'cellchat'){ # add here other file input tools
file <- input$input_file3
req(file)
ext <- tools::file_ext(file$datapath)
validate(need(ext %in% c("csv", "tsv", "xlsx"), "Please choose a file
with the required extension (.csv/.tsv/.xlsx)."))
switch (ext,
csv = {tryCatch({
tab <- read.csv(file$datapath, header = TRUE)
if("X" %in% colnames(tab)){
tab <- tab[, !colnames(tab) == "X"]
}
},
error = function(e) {
# return a safeError if a parsing error occurs
stop(safeError("Error reading input file"))
}
)},
tsv = {tryCatch({
tab <- read.table(file$datapath, sep = "\t",
header = TRUE)
},
error = function(e) {
# return a safeError if a parsing error occurs
stop(safeError("Error reading input file"))
}
)},
xlsx = {tryCatch({
tab <- read_excel(file$datapath, col_names = TRUE)
},
error = function(e) {
# return a safeError if a parsing error occurs
stop(safeError("Error reading input file"))
}
)}
)
# Checks on required columns
req.columns <- c("source", "target", "ligand", "receptor", "prob", "pval",
"interaction_name", "interaction_name_2", "pathway_name",
"annotation", "evidence")
if(!all(req.columns %in% colnames(tab))){
missing.col <- req.columns[!(req.columns %in% colnames(tab))]
shinyalert(text = paste("Looks like these required columns are missing:",
paste(missing.col, collapse = " "), sep = " "),
type = "error",
showCancelButton = FALSE)
} else {
rv$data$db3 <- suppressWarnings(read.cellchat(tab))
shinyalert(text = "Your data was successfully loaded and preprocessed!",
type = "success",
showCancelButton = FALSE)
}
} else if(input$select_input_tool3 == 'icellnet'){
file <- input$input_file3
req(file)
ext <- tools::file_ext(file$datapath)
validate(need(ext %in% c("csv"), "Please choose a file
with the required extension (.csv)."))
switch (ext,
csv = {tryCatch({
tab <- read.csv(file$datapath)
},
error = function(e) {
# return a safeError if a parsing error occurs
stop(safeError("Error reading input file"))
}
)}
)
validate(need(input$icellnet_CC_3, "Please give a name to the central cell!"))
rv$data$db3 <- suppressWarnings(read.icellnet(tab, input$icellnet_CC_3, input$icellnet_dir_3))
shinyalert(text = "Your data was successfully loaded and preprocessed!",
type = "success",
showCancelButton = FALSE)
}
})
return(rv)
})
}
martaint/InterCellar documentation built on April 7, 2022, 11:44 a.m.
R Package Documentation
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Defines functions mod_upload_server mod_upload_ui
#' upload UI Function
#'
#' @description A shiny Module.
#'
#' @param id,input,output,session Internal parameters for {shiny}.
#'
#' @noRd
#'
#' @importFrom shiny NS tagList fluidRow column selectInput conditionalPanel
#' textOutput tabPanel
#' @importFrom shinyFiles shinyDirButton shinyDirChoose getVolumes parseDirPath
#' @importFrom shinydashboard tabBox
#' @importFrom fs path_home
mod_upload_ui <- function(id){
ns <- NS(id)
supported.tools.list <- list("CellPhoneDB v2" = "cpdbv2",
"CellChat" = "cellchat",
"ICELLNET" = "icellnet",
"SingleCellSignalR" = "scsignalR"
)
text.cpdb <- "Please select the output folder generated by CPDB (v2). When the
statistical analysis was run, this folder contains 4 .txt files
(<em>deconvoluted</em>, <em>means</em>, <em>pvalues</em> and
<em>significant_means</em>). In this case, InterCellar will use results stored
in <em>significant_means</em> for further analyses. If no statistical analysis
was run, InterCellar will rely on <em>means</em>."
text.scsignalR <- "Please select the output folder generated by
SingleCellSignalR. This is by default named <em>cell-signaling</em> and
contains a collection of .txt files, one for each clusters pair considered."
text.cellchat <- "InterCellar expects a dataframe consisting of inferred cell-cell
communications at the level of ligand-receptor interactions. This can be obtained
by running CellChat's function <em>subsetCommunication (with param slot.name = 'net')</em>.
We recommend saving this dataframe as a .csv file (quote = FALSE), but .tsv and .xlsx files are also supported."
text.icellnet <- "InterCellar accepts a dataframe obtained by running ICELLNET's function <em>icellnet.score</em>. Please
specifiy the direction of communication ('out' or 'in') and give a name to the <em>central cell</em>. The dataframe should
be saved as a .csv file (with row.names = TRUE)."
tagList(
fluidRow(
column(width = 6,
h2("Upload cell-cell interactions")),
),
fluidRow(
box(width = 12,
title = h3("Analysis setup"),
column(width = 6,
h4("Please select an existing local folder where InterCellar will save all results of your analysis."),
),
column(width = 6,
shinyFiles::shinyDirButton(ns("out_folder"),
"Select folder",
"Please select a folder",
icon = icon("folder")),
verbatimTextOutput(ns("path_out_folder"))
)
)
),
tabBox(
width = NULL,
tabPanel(h4("From supported tools"),
fluidRow(
box(width = 12,
title = "CCI data #1",
status = "primary",
collapsible = TRUE,
solidHeader = TRUE,
column(6,
textInput(ns("db1_name"),
label = h4("CCI data ID"),
placeholder = "my_CCI_data1"),
textInput(ns("db1_out_folder"),
label = h4("Output folder tag"),
value = NULL,
placeholder = "my_out_folder1")
),
column(6,
selectInput(ns("select_input_tool1"),
label = h4("Select tool:"),
choices = supported.tools.list,
multiple = FALSE),
# Conditional panels
conditionalPanel(
condition = "input.select_input_tool1 == 'cpdbv2'",
ns = ns,
p(div(HTML(text.cpdb)))
),
conditionalPanel(
condition = "input.select_input_tool1 == 'scsignalR'",
ns = ns,
p(div(HTML(text.scsignalR)))
),
conditionalPanel(
condition = "input.select_input_tool1 == 'cellchat'",
ns = ns,
p(div(HTML(text.cellchat)))
),
conditionalPanel(
condition = "input.select_input_tool1 == 'icellnet'",
ns = ns,
p(div(HTML(text.icellnet)))
),
conditionalPanel(
condition = "input.select_input_tool1 == 'cpdbv2' | input.select_input_tool1 == 'scsignalR'",
ns = ns,
shinyFiles::shinyDirButton(ns("directory1"),
"Select folder",
"Please select a folder"),
verbatimTextOutput(ns("selected_folder1"))
),
conditionalPanel(
condition = "input.select_input_tool1 == 'cellchat' | input.select_input_tool1 == 'icellnet'",
ns = ns,
fileInput(ns("input_file1"),
"Choose Input File (.csv/.tsv/.xlsx)",
multiple = FALSE,
accept = c(".csv", ".tsv", ".xlsx"))
),
conditionalPanel(
condition = "input.select_input_tool1 == 'icellnet'",
ns = ns,
radioButtons(ns("icellnet_dir_1"),
label = "Select direction:",
choices = list("out", "in"),
inline = TRUE),
textInput(ns("icellnet_CC_1"),
label = "Central cell name",
value = NULL,
placeholder = "B cells")
)
##
),
fluidRow(column(width = 1, offset = 11,
actionButton(ns("input_file_button1"),
label = h4("GO!"),
class = "btn-primary")
))
)),
fluidRow(
box(width = 12,
title = "CCI data #2",
status = "warning",
collapsible = TRUE,
collapsed = TRUE,
solidHeader = TRUE,
column(6,
textInput(ns("db2_name"),
label = h4("CCI data ID"),
placeholder = "my_CCI_data2"),
textInput(ns("db2_out_folder"),
label = h4("Output folder tag"),
value = NULL,
placeholder = "my_out_folder2")
),
column(6,
selectInput(ns("select_input_tool2"),
label = h4("Select tool:"),
choices = supported.tools.list,
multiple = FALSE),
# Conditional panels
conditionalPanel(
condition = "input.select_input_tool2 == 'cpdbv2'",
ns = ns,
p(div(HTML(text.cpdb)))
),
conditionalPanel(
condition = "input.select_input_tool2 == 'scsignalR'",
ns = ns,
p(div(HTML(text.scsignalR)))
),
conditionalPanel(
condition = "input.select_input_tool2 == 'cellchat'",
ns = ns,
p(div(HTML(text.cellchat)))
),
conditionalPanel(
condition = "input.select_input_tool2 == 'icellnet'",
ns = ns,
p(div(HTML(text.icellnet)))
),
conditionalPanel(
condition = "input.select_input_tool2 == 'cpdbv2' | input.select_input_tool2 == 'scsignalR'",
ns = ns,
shinyFiles::shinyDirButton(ns("directory2"),
"Select folder",
"Please select a folder"),
verbatimTextOutput(ns("selected_folder2"))
),
conditionalPanel(
condition = "input.select_input_tool2 == 'cellchat' | input.select_input_tool2 == 'icellnet'",
ns = ns,
fileInput(ns("input_file2"),
"Choose Input File (.csv/.tsv/.xlsx)",
multiple = FALSE,
accept = c(".csv", ".tsv", ".xlsx"))
),
conditionalPanel(
condition = "input.select_input_tool2 == 'icellnet'",
ns = ns,
radioButtons(ns("icellnet_dir_2"),
label = "Select direction:",
choices = list("out", "in"),
inline = TRUE),
textInput(ns("icellnet_CC_2"),
label = "Central cell name",
value = NULL,
placeholder = "B cells")
)
##
),
fluidRow(column(width = 1, offset = 11,
actionButton(ns("input_file_button2"),
label = h4("GO!"),
class = "btn-warning")
))
)),
fluidRow(
box(width = 12,
title = "CCI data #3",
status = "danger",
collapsible = TRUE,
collapsed = TRUE,
solidHeader = TRUE,
column(6,
textInput(ns("db3_name"),
label = h4("CCI data ID"),
placeholder = "my_CCI_data3"),
textInput(ns("db3_out_folder"),
label = h4("Output folder tag"),
value = NULL,
placeholder = "my_out_folder3")
),
column(6,
selectInput(ns("select_input_tool3"),
label = h4("Select tool:"),
choices = supported.tools.list,
multiple = FALSE),
# Conditional panels
conditionalPanel(
condition = "input.select_input_tool3 == 'cpdbv2'",
ns = ns,
p(div(HTML(text.cpdb)))
),
conditionalPanel(
condition = "input.select_input_tool3 == 'scsignalR'",
ns = ns,
p(div(HTML(text.scsignalR)))
),
conditionalPanel(
condition = "input.select_input_tool3 == 'cellchat'",
ns = ns,
p(div(HTML(text.cellchat)))
),
conditionalPanel(
condition = "input.select_input_tool3 == 'icellnet'",
ns = ns,
p(div(HTML(text.icellnet)))
),
conditionalPanel(
condition = "input.select_input_tool3 == 'cpdbv2' | input.select_input_tool3 == 'scsignalR'",
ns = ns,
shinyFiles::shinyDirButton(ns("directory3"),
"Select folder",
"Please select a folder"),
verbatimTextOutput(ns("selected_folder3"))
),
conditionalPanel(
condition = "input.select_input_tool3 == 'cellchat' | input.select_input_tool3 == 'icellnet'",
ns = ns,
fileInput(ns("input_file3"),
"Choose Input File (.csv/.tsv/.xlsx)",
multiple = FALSE,
accept = c(".csv", ".tsv", ".xlsx"))
),
conditionalPanel(
condition = "input.select_input_tool3 == 'icellnet'",
ns = ns,
radioButtons(ns("icellnet_dir_3"),
label = "Select direction:",
choices = list("out", "in"),
inline = TRUE),
textInput(ns("icellnet_CC_3"),
label = "Central cell name",
value = NULL,
placeholder = "B cells")
)
##
),
fluidRow(column(width = 1, offset = 11,
actionButton(ns("input_file_button3"),
label = h4("GO!"),
class = "btn-danger")
))
))
), #tabpanel
tabPanel(h4("From custom analysis"),
mod_upload_custom_ui("upload_custom_ui_1")
)
)#tabbox
)
}
#' upload Server Function
#'
#' @importFrom shinyalert shinyalert
#' @noRd
mod_upload_server <- function(id) {
moduleServer(id, function(input, output, session) {
rv <- reactiveValues(data = list(db1 = NULL,
db2 = NULL,
db3 = NULL),
db_names = list(db1 = NULL,
db2 = NULL,
db3 = NULL),
output_folders_path = list(db1 = NULL,
db2 = NULL,
db3 = NULL),
output_folder = NULL,
output_tags = list(db1 = NULL,
db2 = NULL,
db3 = NULL))
### For supported tools requiring folders
volumes <- c(Home = fs::path_home(), getVolumes()())
## CCI data 1
shinyDirChoose(input, "directory1", roots = volumes, session = session,
restrictions = system.file(package = "base"))
input_folder1 <- reactive({
req(input$directory1)
parseDirPath(volumes, input$directory1)
})
output$selected_folder1 <- renderText({
input_folder1()
})
## CCI data 2
shinyDirChoose(input, "directory2", roots = volumes, session = session,
restrictions = system.file(package = "base"))
input_folder2 <- reactive({
req(input$directory2)
parseDirPath(volumes, input$directory2)
})
output$selected_folder2 <- renderText({
input_folder2()
})
## CCI data 3
shinyDirChoose(input, "directory3", roots = volumes, session = session,
restrictions = system.file(package = "base"))
input_folder3 <- reactive({
req(input$directory3)
parseDirPath(volumes, input$directory3)
})
output$selected_folder3 <- renderText({
input_folder3()
})
### Output folder
shinyDirChoose(input, "out_folder", roots = volumes, session = session,
restrictions = system.file(package = "base"))
output_folder <- reactive({
#req(input$out_folder)
parseDirPath(volumes, input$out_folder)
})
output$path_out_folder <- renderText({
output_folder()
})
observeEvent(output_folder(), {
rv$output_folder <- output_folder()
})
### CCI data 1
### Read input and construct datatable
observeEvent(input$input_file_button1, {
if(input$db1_name == ""){
shinyalert(text = "Please specify an ID for your CCI data #1!", type = "error",
showCancelButton = FALSE)
}
if(input$db1_out_folder == ""){
shinyalert(text = "Please specify an output folder tag for your CCI data #1!", type = "error",
showCancelButton = FALSE)
}
if(identical(output_folder(), character(0))){
shinyalert(text = "Please select an output folder!",
type = "error",
showCancelButton = FALSE)
}
req(output_folder())
req(input$db1_name, input$db1_out_folder)
#check that tags are not repeated
tags <- c(input$db1_out_folder, input$db2_out_folder, input$db3_out_folder)
tags <- tags[!(tags == "")]
if(any(duplicated(tags))){
shinyalert(text = "It looks like tags for output folders are not unique! Please re-upload your data after changing repeated tags
to avoid overwriting results!",
type = "error",
showCancelButton = FALSE)
} else {
# create directory with tags
dir.create(file.path(output_folder(), paste0("InterCellar_results_", input$db1_out_folder)))
shinyalert(text = paste0("Directory created: ", file.path(output_folder(), paste0("InterCellar_results_", input$db1_out_folder))),
type = "success",
showCancelButton = FALSE,
timer = 4000)
rv$output_folders_path$db1 <- file.path(output_folder(), paste0("InterCellar_results_", input$db1_out_folder))
}
rv$db_names$db1 <- as.character(input$db1_name)
rv$output_tags$db1 <- input$db1_out_folder
if(input$select_input_tool1 == 'cpdbv2'){
req(input_folder1())
files <- list.files(input_folder1())
if("means.txt" %in% files){
rv$data$db1 <- read.CPDBv2(folder = input_folder1())
shinyalert(text = "Your data was successfully loaded and preprocessed!",
type = "success",
showCancelButton = FALSE)
} else {
shinyalert(text = "The selected folder does not contain CPDB output files!
Please select the correct folder.",
type = "error",
showCancelButton = FALSE)
}
}
else if(input$select_input_tool1 == 'scsignalR'){
req(input_folder1())
files <- list.files(input_folder1())
if(all(grep("LR_interactions", files))){
rv$data$db1 <- read.SCsignalR(folder = input_folder1())
shinyalert(text = "Your data was successfully loaded and preprocessed!",
type = "success",
showCancelButton = FALSE)
} else{
shinyalert(text = "The selected folder does not contain
SingleCellSignalR output files!
Please select the correct folder.",
type = "error",
showCancelButton = FALSE)
}
} else if(input$select_input_tool1 == 'cellchat'){
file <- input$input_file1
req(file)
ext <- tools::file_ext(file$datapath)
validate(need(ext %in% c("csv", "tsv", "xlsx"), "Please choose a file
with the required extension (.csv/.tsv/.xlsx)."))
switch (ext,
csv = {tryCatch({
tab <- read.csv(file$datapath, header = TRUE)
if("X" %in% colnames(tab)){
tab <- tab[, !colnames(tab) == "X"]
}
},
error = function(e) {
# return a safeError if a parsing error occurs
stop(safeError("Error reading input file"))
}
)},
tsv = {tryCatch({
tab <- read.table(file$datapath, sep = "\t",
header = TRUE)
},
error = function(e) {
# return a safeError if a parsing error occurs
stop(safeError("Error reading input file"))
}
)},
xlsx = {tryCatch({
tab <- read_excel(file$datapath, col_names = TRUE)
},
error = function(e) {
# return a safeError if a parsing error occurs
stop(safeError("Error reading input file"))
}
)}
)
# Checks on required columns
req.columns <- c("source", "target", "ligand", "receptor", "prob", "pval",
"interaction_name", "interaction_name_2", "pathway_name",
"annotation", "evidence")
if(!all(req.columns %in% colnames(tab))){
missing.col <- req.columns[!(req.columns %in% colnames(tab))]
shinyalert(text = paste("Looks like these required columns are missing:",
paste(missing.col, collapse = " "), sep = " "),
type = "error",
showCancelButton = FALSE)
} else {
rv$data$db1 <- suppressWarnings(read.cellchat(tab))
shinyalert(text = "Your data was successfully loaded and preprocessed!",
type = "success",
showCancelButton = FALSE)
}
} else if(input$select_input_tool1 == 'icellnet'){
file <- input$input_file1
req(file)
ext <- tools::file_ext(file$datapath)
validate(need(ext %in% c("csv"), "Please choose a file
with the required extension (.csv)."))
switch (ext,
csv = {tryCatch({
tab <- read.csv(file$datapath)
},
error = function(e) {
# return a safeError if a parsing error occurs
stop(safeError("Error reading input file"))
}
)}
)
validate(need(input$icellnet_CC_1, "Please give a name to the central cell!"))
rv$data$db1 <- suppressWarnings(read.icellnet(tab, input$icellnet_CC_1, input$icellnet_dir_1))
shinyalert(text = "Your data was successfully loaded and preprocessed!",
type = "success",
showCancelButton = FALSE)
}
})
### CCI data 2
### Read input and construct datatable
observeEvent(input$input_file_button2, {
if(input$db2_name == ""){
shinyalert(text = "Please specify an ID for your CCI data #2!", type = "error",
showCancelButton = FALSE)
}
if(input$db2_out_folder == ""){
shinyalert(text = "Please specify an output folder tag for your CCI data #2!", type = "error",
showCancelButton = FALSE)
}
if(identical(output_folder(), character(0))){
shinyalert(text = "Please select an output folder!",
type = "error",
showCancelButton = FALSE)
}
req(output_folder())
req(input$db2_name, input$db2_out_folder)
#check that tags are not repeated
tags <- c(input$db1_out_folder, input$db2_out_folder, input$db3_out_folder)
tags <- tags[!(tags == "")]
if(any(duplicated(tags))){
shinyalert(text = "It looks like tags for output folders are not unique! Please re-upload your data after changing repeated tags
to avoid overwriting results!",
type = "error",
showCancelButton = FALSE)
} else {
# create directory with tags
dir.create(file.path(output_folder(), paste0("InterCellar_results_", input$db2_out_folder)))
shinyalert(text = paste0("Directory created: ", file.path(output_folder(), paste0("InterCellar_results_", input$db2_out_folder))),
type = "success",
showCancelButton = FALSE,
timer = 4000)
rv$output_folders_path$db2 <- file.path(output_folder(), paste0("InterCellar_results_", input$db2_out_folder))
}
rv$db_names$db2 <- as.character(input$db2_name)
rv$output_tags$db2 <- input$db2_out_folder
if(input$select_input_tool2 == 'cpdbv2'){
req(input_folder2())
files <- list.files(input_folder2())
if("means.txt" %in% files){
rv$data$db2 <- read.CPDBv2(folder = input_folder2())
shinyalert(text = "Your data was successfully loaded and preprocessed!",
type = "success",
showCancelButton = FALSE)
} else {
shinyalert(text = "The selected folder does not contain CPDB output files!
Please select the correct folder.",
type = "error",
showCancelButton = FALSE)
}
}
else if(input$select_input_tool2 == 'scsignalR'){
req(input_folder2())
files <- list.files(input_folder2())
if(all(grep("LR_interactions", files))){
rv$data$db2 <- read.SCsignalR(folder = input_folder2())
shinyalert(text = "Your data was successfully loaded and preprocessed!",
type = "success",
showCancelButton = FALSE)
} else{
shinyalert(text = "The selected folder does not contain
SingleCellSignalR output files!
Please select the correct folder.",
type = "error",
showCancelButton = FALSE)
}
} else if(input$select_input_tool2 == 'cellchat'){ # add here other file input tools
file <- input$input_file2
req(file)
ext <- tools::file_ext(file$datapath)
validate(need(ext %in% c("csv", "tsv", "xlsx"), "Please choose a file
with the required extension (.csv/.tsv/.xlsx)."))
switch (ext,
csv = {tryCatch({
tab <- read.csv(file$datapath, header = TRUE)
if("X" %in% colnames(tab)){
tab <- tab[, !colnames(tab) == "X"]
}
},
error = function(e) {
# return a safeError if a parsing error occurs
stop(safeError("Error reading input file"))
}
)},
tsv = {tryCatch({
tab <- read.table(file$datapath, sep = "\t",
header = TRUE)
},
error = function(e) {
# return a safeError if a parsing error occurs
stop(safeError("Error reading input file"))
}
)},
xlsx = {tryCatch({
tab <- read_excel(file$datapath, col_names = TRUE)
},
error = function(e) {
# return a safeError if a parsing error occurs
stop(safeError("Error reading input file"))
}
)}
)
# Checks on required columns
req.columns <- c("source", "target", "ligand", "receptor", "prob", "pval",
"interaction_name", "interaction_name_2", "pathway_name",
"annotation", "evidence")
if(!all(req.columns %in% colnames(tab))){
missing.col <- req.columns[!(req.columns %in% colnames(tab))]
shinyalert(text = paste("Looks like these required columns are missing:",
paste(missing.col, collapse = " "), sep = " "),
type = "error",
showCancelButton = FALSE)
} else {
rv$data$db2 <- suppressWarnings(read.cellchat(tab))
shinyalert(text = "Your data was successfully loaded and preprocessed!",
type = "success",
showCancelButton = FALSE)
}
} else if(input$select_input_tool2 == 'icellnet'){
file <- input$input_file2
req(file)
ext <- tools::file_ext(file$datapath)
validate(need(ext %in% c("csv"), "Please choose a file
with the required extension (.csv)."))
switch (ext,
csv = {tryCatch({
tab <- read.csv(file$datapath)
},
error = function(e) {
# return a safeError if a parsing error occurs
stop(safeError("Error reading input file"))
}
)}
)
validate(need(input$icellnet_CC_2, "Please give a name to the central cell!"))
rv$data$db2 <- suppressWarnings(read.icellnet(tab, input$icellnet_CC_2, input$icellnet_dir_2))
shinyalert(text = "Your data was successfully loaded and preprocessed!",
type = "success",
showCancelButton = FALSE)
}
})
### CCI data 3
### Read input and construct datatable
observeEvent(input$input_file_button3, {
if(input$db3_name == ""){
shinyalert(text = "Please specify an ID for your CCI data #3!", type = "error",
showCancelButton = FALSE)
}
if(input$db3_out_folder == ""){
shinyalert(text = "Please specify an output folder tag for your CCI data #3!", type = "error",
showCancelButton = FALSE)
}
if(identical(output_folder(), character(0))){
shinyalert(text = "Please select an output folder!",
type = "error",
showCancelButton = FALSE)
}
req(output_folder())
req(input$db3_name, input$db3_out_folder)
#check that tags are not repeated
tags <- c(input$db1_out_folder, input$db2_out_folder, input$db3_out_folder)
tags <- tags[!(tags == "")]
if(any(duplicated(tags))){
shinyalert(text = "It looks like tags for output folders are not unique! Please re-upload your data after changing repeated tags
to avoid overwriting results!",
type = "error",
showCancelButton = FALSE)
} else {
# create directory with tags
dir.create(file.path(output_folder(), paste0("InterCellar_results_", input$db3_out_folder)))
shinyalert(text = paste0("Directory created: ", file.path(output_folder(), paste0("InterCellar_results_", input$db3_out_folder))),
type = "success",
showCancelButton = FALSE,
timer = 4000)
rv$output_folders_path$db3 <- file.path(output_folder(), paste0("InterCellar_results_", input$db3_out_folder))
}
rv$db_names$db3 <- as.character(input$db3_name)
rv$output_tags$db3 <- input$db3_out_folder
if(input$select_input_tool3 == 'cpdbv2'){
req(input_folder3())
files <- list.files(input_folder3())
if("means.txt" %in% files){
rv$data$db3 <- read.CPDBv2(folder = input_folder3())
shinyalert(text = "Your data was successfully loaded and preprocessed!",
type = "success",
showCancelButton = FALSE)
} else {
shinyalert(text = "The selected folder does not contain CPDB output files!
Please select the correct folder.",
type = "error",
showCancelButton = FALSE)
}
}
else if(input$select_input_tool3 == 'scsignalR'){
req(input_folder3())
files <- list.files(input_folder3())
if(all(grep("LR_interactions", files))){
rv$data$db3 <- read.SCsignalR(folder = input_folder3())
shinyalert(text = "Your data was successfully loaded and preprocessed!",
type = "success",
showCancelButton = FALSE)
} else{
shinyalert(text = "The selected folder does not contain
SingleCellSignalR output files!
Please select the correct folder.",
type = "error",
showCancelButton = FALSE)
}
} else if(input$select_input_tool3 == 'cellchat'){ # add here other file input tools
file <- input$input_file3
req(file)
ext <- tools::file_ext(file$datapath)
validate(need(ext %in% c("csv", "tsv", "xlsx"), "Please choose a file
with the required extension (.csv/.tsv/.xlsx)."))
switch (ext,
csv = {tryCatch({
tab <- read.csv(file$datapath, header = TRUE)
if("X" %in% colnames(tab)){
tab <- tab[, !colnames(tab) == "X"]
}
},
error = function(e) {
# return a safeError if a parsing error occurs
stop(safeError("Error reading input file"))
}
)},
tsv = {tryCatch({
tab <- read.table(file$datapath, sep = "\t",
header = TRUE)
},
error = function(e) {
# return a safeError if a parsing error occurs
stop(safeError("Error reading input file"))
}
)},
xlsx = {tryCatch({
tab <- read_excel(file$datapath, col_names = TRUE)
},
error = function(e) {
# return a safeError if a parsing error occurs
stop(safeError("Error reading input file"))
}
)}
)
# Checks on required columns
req.columns <- c("source", "target", "ligand", "receptor", "prob", "pval",
"interaction_name", "interaction_name_2", "pathway_name",
"annotation", "evidence")
if(!all(req.columns %in% colnames(tab))){
missing.col <- req.columns[!(req.columns %in% colnames(tab))]
shinyalert(text = paste("Looks like these required columns are missing:",
paste(missing.col, collapse = " "), sep = " "),
type = "error",
showCancelButton = FALSE)
} else {
rv$data$db3 <- suppressWarnings(read.cellchat(tab))
shinyalert(text = "Your data was successfully loaded and preprocessed!",
type = "success",
showCancelButton = FALSE)
}
} else if(input$select_input_tool3 == 'icellnet'){
file <- input$input_file3
req(file)
ext <- tools::file_ext(file$datapath)
validate(need(ext %in% c("csv"), "Please choose a file
with the required extension (.csv)."))
switch (ext,
csv = {tryCatch({
tab <- read.csv(file$datapath)
},
error = function(e) {
# return a safeError if a parsing error occurs
stop(safeError("Error reading input file"))
}
)}
)
validate(need(input$icellnet_CC_3, "Please give a name to the central cell!"))
rv$data$db3 <- suppressWarnings(read.icellnet(tab, input$icellnet_CC_3, input$icellnet_dir_3))
shinyalert(text = "Your data was successfully loaded and preprocessed!",
type = "success",
showCancelButton = FALSE)
}
})
return(rv)
})
}
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