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Add average transcripts of each gene
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@dyxmvp
dyxmvp committed Feb 24, 2019
1 parent 8c870a5 commit ccb0493
Showing 1 changed file with 48 additions and 15 deletions.
63 changes: 48 additions & 15 deletions inst/shiny/quick_look.R
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@ lookUI <- function(id) {

selectizeInput(ns("look_filetype"), label="Select a file type",
choices = c("DGE files (*.dge.*)" = "dge_look",
"Combined file (*.txt*)" = "combined_look"
"Combined files (*.txt*)" = "combined_look"
),
selected = c("DGE files (*.dge.*)"), multiple = FALSE),

Expand All @@ -28,10 +28,15 @@ lookUI <- function(id) {
),

conditionalPanel(condition = "input.look_filetype == 'combined_look'",
tags$b("Select a combined file:"),
tags$b("Select a cell fraction file:"),
tags$p(),
verbatimTextOutput(ns("combined_files_look"), placeholder = TRUE),
shinyFilesButton(ns("file_combined_look"), "Select a combined file", "Please select a file", multiple = FALSE),
shinyFilesButton(ns("file_combined_look"), "Select a cell fraction file", "Please select a file", multiple = FALSE),
tags$p(),
tags$b("Select an average transcripts file:"),
tags$p(),
verbatimTextOutput(ns("avg_files_look"), placeholder = TRUE),
shinyFilesButton(ns("file_avg_look"), "Select an average transcripts file", "Please select a file", multiple = FALSE),
tags$p(),
ns = NS(id)
),
Expand Down Expand Up @@ -61,12 +66,12 @@ lookUI <- function(id) {
),

box(
title = "Gene plots", width = 12, status = "primary", collapsible = T,
title = "Percentage of cells expressing selected genes", width = 12, status = "primary", collapsible = T,
uiOutput(ns("gene_plots_look"))
),

box(
title = "Gene table", width = 12, status = "info", collapsible = T,
title = "Average number of transcripts each gene expressed", width = 12, status = "info", collapsible = T,
uiOutput(ns("gene_table_look"))
)

Expand Down Expand Up @@ -110,13 +115,17 @@ lookServer <- function(input, output, session, fileRoot = NULL) {

shinyFileChoose(input, "file_samples_look", roots = volumes, session = session, filetypes=c('', 'txt', 'gz'))
shinyFileChoose(input, "file_combined_look", roots = volumes, session = session, filetypes=c('', 'txt'))
shinyFileChoose(input, "file_avg_look", roots = volumes, session = session, filetypes=c('', 'txt'))

output$samples_files_look <- renderPrint({
as.character(parseFilePaths(volumes, input$file_samples_look)[4])
})
output$combined_files_look <- renderPrint({
as.character(parseFilePaths(volumes, input$file_combined_look)[4])
})
output$avg_files_look <- renderPrint({
as.character(parseFilePaths(volumes, input$file_avg_look)[4])
})

# Upload data
observeEvent(input$do_upload, {
Expand Down Expand Up @@ -146,22 +155,31 @@ lookServer <- function(input, output, session, fileRoot = NULL) {
lapply(sample_list, upload_dges)

if(length(sample_list) > 1){

df_merge <<- df_merge[, -1]
df_merge_avg <<- df_merge_avg[, -1]
}

df_merge[is.na(df_merge)] <- 0
df_merge_avg[is.na(df_merge_avg)] <- 0

write.table(df_merge, file.path(dirname(sample_list[1]), "combined.txt"), append = FALSE, sep = "\t", dec = ".",
write.table(df_merge, file.path(dirname(sample_list[1]), "cell_frac.txt"), append = FALSE, sep = "\t", dec = ".",
row.names = TRUE, col.names = TRUE)
write.table(df_merge_avg, file.path(dirname(sample_list[1]), "genes_avg.txt"), append = FALSE, sep = "\t", dec = ".",
row.names = TRUE, col.names = TRUE)
}
else{

sample_list <<- isolate(as.character(parseFilePaths(volumes, input$file_combined_look)$datapath))
df_merge <<- read.table(sample_list, header = T, row.names = 1, stringsAsFactors = F)

sample_list_avg <- isolate(as.character(parseFilePaths(volumes, input$file_avg_look)$datapath))
df_merge_avg <<- read.table(sample_list_avg, header = T, row.names = 1, stringsAsFactors = F)
}

setProgress(value = 0.6)

output$look_gene_table <- renderDT(datatable(df_merge, rownames = TRUE, selection = "none"))
output$look_gene_table <- renderDT(datatable(df_merge_avg, rownames = TRUE, selection = "none"))

setProgress(value = 1)
shinyjs::hide("load_upload")
Expand All @@ -170,7 +188,7 @@ lookServer <- function(input, output, session, fileRoot = NULL) {
})# Upload data END


# plots and table
# plots
observeEvent(input$do_look, {

withProgress(message = "Please wait ...",{
Expand Down Expand Up @@ -212,7 +230,7 @@ lookServer <- function(input, output, session, fileRoot = NULL) {
shinyjs::hide("load_quick_look")
shinyjs::show("check_quick_look")
})
})# plots and table END
})# plots END


output$figure_save_look <- renderUI({
Expand Down Expand Up @@ -246,24 +264,39 @@ lookServer <- function(input, output, session, fileRoot = NULL) {

######################### Gene fraction Start ##########################################
df_merge <<- data.frame(empty_name=character(), stringsAsFactors=FALSE)
df_merge_avg <<- data.frame(empty_name=character(), stringsAsFactors=FALSE)

upload_dges <- function(sample_file){

#Input separated dge files. Returns combined df.
# Input separated dge files. Returns combined df.
sample_name <- sub(pattern = "(.*?)\\..*$", replacement = "\\1", basename(sample_file))

df <- read.table(sample_file, header = T, row.names = 1, stringsAsFactors = F)

df_avg <- data.frame(lapply(rowMeans(df!=0), round, 2))
# Calculate percentage of cells expressing all genes
df_frac <- data.frame(lapply(rowMeans(df!=0), round, 2))
df_frac <- t(df_frac)
colnames(df_frac) <- sample_name
rownames(df_frac) <- rownames(df)

if(length(sample_list) == 1){
df_merge <<- df_frac
}
else{
df_merge <<- transform(merge(df_merge, df_frac, by = 0, all = TRUE), row.names = Row.names, Row.names = NULL)
}

# Calculate the average transcripts of each gene expressed
df_avg <- data.frame(lapply(rowMeans(df), round, 2))
df_avg <- t(df_avg)
colnames(df_avg) <- paste0(sample_name, "_avg")
rownames(df_avg) <- rownames(df)

if(length(sample_list) == 1){
df_merge <<- df_avg
df_merge_avg <<- df_avg
}
else{
df_merge <<- transform(merge(df_merge, df_avg, by = 0, all = TRUE), row.names = Row.names, Row.names = NULL)
df_merge_avg <<- transform(merge(df_merge_avg, df_avg, by = 0, all = TRUE), row.names = Row.names, Row.names = NULL)
}
}

Expand All @@ -278,10 +311,10 @@ gene_frac_plot <- function(sample_name){

df$gene_list <-factor(df$gene_list, levels = genes_look)

p <- ggplot(data = df, aes(x = gene_list, y = gene_frac)) + #scale_x_discrete(limits = genes_look) +
p <- ggplot(data = df, aes(x = gene_list, y = gene_frac)) + # scale_x_discrete(limits = genes_look) +
geom_bar(stat = "identity", fill = "steelblue", width = width_bar) + coord_flip() + theme_minimal() +
geom_text(aes(label = gene_frac), vjust = -0.5, angle = -90, size = 3.5) +
labs(title = sub("_avg$", "", sample_name)) + theme_bw() +
labs(title = sample_name) + theme_bw() + # labs(title = sub("_avg$", "", sample_name))
theme(axis.title.x = element_blank(), axis.title.y = element_blank(),
panel.grid = element_blank(), plot.title = element_text(hjust = 0.5),
axis.text = element_text(size = 10)) +
Expand Down

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