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DGEList object is succesfully created.
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@goknurginer
goknurginer committed Oct 6, 2024
1 parent e4dd3db commit 4dfc461
Showing 1 changed file with 54 additions and 119 deletions.
173 changes: 54 additions & 119 deletions R/app.R
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Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,9 @@ library(tidyverse)
library(readr)
library(edgeR)

# Set maximum upload size to 1 GB
options(shiny.maxRequestSize = 1000 * 1024^2)

# Define a function to read files and render DataTable
read_file_and_render <- function(file_input) {
req(file_input) # Ensure the file is uploaded
Expand All @@ -16,37 +19,24 @@ read_file_and_render <- function(file_input) {

# Read file based on extension and detect separator if necessary
df <- switch(file_ext,
"csv" = read.table(file_input$datapath, check.names = FALSE, sep = ","),
"tsv" = read.table(file_input$datapath, check.names = FALSE, sep = "\t"),
"csv" = read.table(file_input$datapath, check.names = FALSE, sep = ",", header = TRUE),
"tsv" = read.table(file_input$datapath, check.names = FALSE, sep = "\t", header = TRUE),
"txt" = {
# Detect separator for .txt files
first_line <- readLines(file_input$datapath, n = 1)
if (grepl("\t", first_line)) {
read.table(file_input$datapath, check.names = FALSE, sep = "\t")
read.table(file_input$datapath, check.names = FALSE, sep = "\t", header = TRUE)
} else {
read.table(file_input$datapath, check.names = FALSE, sep = " ")
read.table(file_input$datapath, check.names = FALSE, sep = " ", header = TRUE)
}
},
stop("Unsupported file type"))

datatable(df) # Render the DataTable
}

# Define a function to read Fastq files and prepare for display
read_fastq_file <- function(fastq_input) {
req(fastq_input)

# Read the Fastq file. Assuming a simple extraction for demonstration.
fastq_lines <- readLines(fastq_input$datapath)
fastq_data <- data.frame(
ID = fastq_lines[seq(1, length(fastq_lines), by = 4)],
Sequence = fastq_lines[seq(2, length(fastq_lines), by = 4)],
Plus = fastq_lines[seq(3, length(fastq_lines), by = 4)],
Quality = fastq_lines[seq(4, length(fastq_lines), by = 4)],
stringsAsFactors = FALSE
)

datatable(fastq_data)
# Set column names for the guide library if applicable
if (file_ext %in% c("tsv", "csv", "txt")) {
#colnames(df) <- c("sgRNA_ID", "sgRNA_sequence", "gene_ID") # Assigning appropriate names
}
df
}

# Define UI
Expand Down Expand Up @@ -100,11 +90,7 @@ ui <- navbarPage("CuReSPR", id = "main", theme = shinytheme("cerulean"),
),
conditionalPanel(condition = "input.count_matrix_yes_no == 'no'",
h4("Upload fastq files"),
fileInput("upload", label = "", accept = c('.fastq', 'fastq.gz'), multiple = TRUE),
checkboxInput("paired", label = "Fastq files are paired-end"),
checkboxInput("tech", "There are technical replicates"),
checkboxInput("bio", "There are biological replicates"),
actionButton("viewfiles", "View file details")
fileInput("upload", label = "", accept = c('.fastq', 'fastq.gz'), multiple = TRUE)
)
)
),
Expand All @@ -116,16 +102,14 @@ ui <- navbarPage("CuReSPR", id = "main", theme = shinytheme("cerulean"),
),
conditionalPanel(condition = "input.viewsamples > 0",
hr(),
h4("Sample Information"),
h4("Sample information"),
DT::dataTableOutput("dataTableSamples")
),
conditionalPanel(condition = "input.count_matrix_yes_no == 'no' && input.viewfiles > 0",
conditionalPanel(condition = "input.count_matrix_yes_no == 'no'",
hr(),
h4("Enter sample details"),
helpText("Please enter the details about the samples in the following table."),
DT::dataTableOutput("dataTableFiles"),
verbatimTextOutput('sel'),
actionButton("gotocounting", "Go to counting")
h4("Here are the uploaded Fastq files"),
verbatimTextOutput("fastqFilesOutput"),
actionButton("gotocountingfastq", "Go to Counting") # Button to go to counting
),
conditionalPanel(condition = "input.count_matrix_yes_no == 'yes' && input.viewcounts > 0",
hr(),
Expand Down Expand Up @@ -157,7 +141,8 @@ ui <- navbarPage("CuReSPR", id = "main", theme = shinytheme("cerulean"),
actionButton("create_dgelist", "Create DGEList")
),
mainPanel(
textOutput("dgelist_status") # Display status for DGEList creation
textOutput("dgelist_status"), # Display status for DGEList creation
verbatimTextOutput("dge_list_output") # Output for DGEList
)
)
),
Expand All @@ -168,96 +153,41 @@ ui <- navbarPage("CuReSPR", id = "main", theme = shinytheme("cerulean"),

# Define server logic
server <- function(input, output, session) {
# Reactive values to store the uploaded guides and sample information
data_upload_output <- reactiveValues(uploadguides = NULL, viewguides = NULL)
observeEvent(input$viewguides, {
data_upload_output$uploadguides <- input$uploadguides
data_upload_output$viewguides <- TRUE
})

sample_upload_output <- reactiveValues(uploadsamples = NULL, viewsamples = NULL)
observeEvent(input$viewsamples, {
sample_upload_output$uploadsamples <- input$uploadsamples
sample_upload_output$viewsamples <- TRUE
})
# Reactive value to track Fastq file upload
fastq_uploaded <- reactiveVal(FALSE)

myData <- reactiveVal(data.frame(Fastq = character(), Size = numeric(), Group = character()))
observeEvent(input$viewfiles, {
# Fastq file upload output
output$fastqFilesOutput <- renderPrint({
req(input$upload)
test <- sapply(1:nrow(input$upload), function(i) {
as.character(selectInput(paste0("sel", i), "", choices = unique(req(myData()$Group)), width = "100px"))
})
newEntry <- data.frame(Fastq = input$upload[, 1],
Size = input$upload[, 2],
Group = test,
stringsAsFactors = FALSE)
myData(newEntry)
fastq_file_names <- input$upload$name
fastq_uploaded(TRUE) # Mark Fastq files as uploaded
paste("Uploaded Fastq files:", paste(fastq_file_names, collapse = ", "))
})

base_data <- reactive({
if (as.logical(input$paired)) {
myData() %>% add_column(FastqPair = rep(1, nrow(myData())))
} else {
myData()
}
})

v <- reactive({
result <- base_data()
if (as.logical(input$tech)) {
result <- result %>% add_column(TechRep = rep(1, nrow(myData())))
}
if (as.logical(input$bio)) {
result <- result %>% add_column(BioRep = rep(1, nrow(myData())))
}
result
})

output$dataTableFiles <- DT::renderDataTable(
v(),
editable = TRUE,
escape = FALSE,
selection = 'none',
server = FALSE,
options = list(dom = 't', paging = FALSE, ordering = FALSE),
callback = JS("table.rows().every(function(i, tab, row) {
var $this = $(this.node());
$this.attr('id', this.data()[0]);
$this.addClass('shiny-input-container');
});
Shiny.unbindAll(table.table().node());
Shiny.bindAll(table.table().node());")
)

# Render DataTables for uploaded files

observeEvent(input$viewcounts, {
output$dataTableCounts <- DT::renderDataTable({
read_file_and_render(input$uploadcounts)
req(input$uploadcounts) # Ensure a file is uploaded
datatable(read_file_and_render(input$uploadcounts))
})
})

observeEvent(input$viewsamples, {
output$dataTableSamples <- DT::renderDataTable({
read_file_and_render(input$uploadsamples)
req(input$uploadsamples) # Ensure a file is uploaded
datatable(read_file_and_render(input$uploadsamples))
})
})

observeEvent(input$viewguides, {
output$dataTableGuides <- DT::renderDataTable({
read_file_and_render(input$uploadguides)
})
})

observeEvent(input$viewfiles, {
output$dataTableFastq <- DT::renderDataTable({
read_fastq_file(input$upload)
req(input$uploadguides) # Ensure a file is uploaded
datatable(read_file_and_render(input$uploadguides))
})
})

output$sel <- renderPrint({
str(sapply(1:nrow(myData()), function(i) input[[paste0("sel", i)]]))
})

# Handling dynamic UI for group names
output$groupnames <- renderUI({
groupnames <- lapply(1:input$num, function(i) {
Expand All @@ -272,8 +202,8 @@ server <- function(input, output, session) {
paste("Groups are:", paste(group_values, collapse = ", "))
})

observeEvent(input$gotocounting, {
updateTabsetPanel(session, "inTabset", selected = "Counting")
observeEvent(input$gotocountingfastq, {
updateTabsetPanel(session, "inTabset", selected = "Counting") # Navigate to Counting tab after Fastq files loaded
})

observeEvent(input$gotopreprocessing, {
Expand All @@ -283,10 +213,9 @@ server <- function(input, output, session) {
# Counting functionality
observeEvent(input$guidecounts, {
output$status <- renderText("Calculating guide counts...")
req(data_upload_output$uploadguides)
req(input$uploadguides)

# Here you would add logic for the counting process
# This is just a placeholder to show you might generate counts
# This is just a placeholder. Add logic for the counting process with Rsubread, MAGeCK, etc. later.
count_data <- data.frame(
sgRNA_ID = c("sgRNA1", "sgRNA2"),
Count = c(100, 200) # Sample count data; replace with actual counting logic
Expand Down Expand Up @@ -324,17 +253,23 @@ server <- function(input, output, session) {
}
)

# Status for DGEList creation
output$dgelist_status <- renderText({
req(input$create_dgelist) # Ensure the button was clicked
if (is.null(data_upload_output$uploadcounts) ||
is.null(data_upload_output$uploadguides) ||
is.null(data_upload_output$uploadsamples)) {
return("Please ensure all required files are uploaded.")
}
# DGEList creation
observeEvent(input$create_dgelist, {
req(input$uploadcounts, input$uploadsamples) # Ensure necessary files are uploaded

# Create the DGEList object
dge <- DGEList(counts = read_file_and_render(input$uploadcounts)[,-c(1:2)],
genes = read_file_and_render(input$uploadguides),
samples = read_file_and_render(input$uploadsamples))
dge$samples$group <- dge$samples$Groups
dge$samples$Groups <- NULL
rownames(dge) <- read_file_and_render(input$uploadcounts)[,1]
# Print the DGEList output in the Preprocessing tab
output$dge_list_output <- renderPrint({
dge # Display the DGEList object
})

# Here you would implement the DGEList creation logic
return("DGEList created successfully!") # Update this to reflect actual status
output$dgelist_status <- renderText("DGEList created successfully!")
})
}

Expand Down

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