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study_plots_ct_umap.R
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study_plots_ct_umap.R
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# bsub -q new-medium -R "select[model=Intel_Skylake] rusage[mem=32000]" -oo log/study_plots_ct_umap.o -eo log/study_plots_ct_umap.e Rscript study_plots_ct_umap.R
library(data.table)
library(ggplot2)
library(magrittr)
library(Matrix)
library(stringr)
library(plyr)
library(cowplot)
library(RColorBrewer)
library(scales)
library(matkot)
try(library(randomcoloR), silent = TRUE)
source('functions.R')
paths_table <- fread('../data/paths_table.csv', encoding = 'UTF-8', key = c('study', 'cancer_type'))
for(r in transpose(as.list(unique(paths_table[, .(study, cancer_type)])))) {
cat(r, '\n')
if(all(c('data_ct_umap.RDS', 'UMAP.pdf') %in% dir(paste0('../data/study_plots/', gsub('/', '-', r[2]), '/', r[1])) == c(TRUE, FALSE))) {
plot_data <- readRDS(paste0('../data/study_plots/', gsub('/', '-', r[2]), '/', r[1], '/data_ct_umap.RDS'))
nullcond <- sapply(plot_data, function(x) ifelse(is.null(x), TRUE, is.null(x$data)))
if(all(nullcond)) next
if('randomcoloR' %in% .packages(TRUE)) {
set.seed(9728)
plot_colours <- lapply(
which(!nullcond),
function(i) {
pdata <- plot_data[[i]]$data
slapply(c('cell_type', 'sample')[c('cell_type', 'sample') %in% names(pdata)], function(vn) unique(pdata[[vn]]))
}
)
plot_colours <- slapply(
c('cell_type', 'sample'),
function(vn) {
vn_unique <- unique(unlist(lapply(plot_colours, function(x) if(vn %in% names(x)) x[[vn]])))
if(!is.null(vn_unique)) setNames(distinctColorPalette(length(vn_unique)), vn_unique)
}
)
}
out <- lapply(which(!nullcond), function(i) {
pdata <- plot_data[[i]]$data
if(!any(c('cell_type', 'sample') %in% names(pdata))) return(NULL)
# To use in plot titles:
if(sum(unique(paths_table[, .(study, cancer_type)])$study == r[1]) == 1) {
if(paths_table[as.list(r), .N] > 1) {
title_tail <- paste0(r[1], ' - ', paths_table[as.list(r)][i, if(group_name == '') paste('Group', group) else group_name])
} else {
title_tail <- r[1]
}
} else {
if(paths_table[as.list(r), .N] > 1) {
title_tail <- paste0(r[1], ', ', r[2], ' - ', paths_table[as.list(r)][i, if(group_name == '') paste('Group', group) else
group_name])
} else {
title_tail <- paste0(r[1], ', ', r[2])
}
}
if('cell_type' %in% names(pdata)) {
if('Malignant' %in% pdata$cell_type) {
pdata[, cell_type := factor(cell_type, levels = c('Malignant', sort(unique(cell_type[cell_type != 'Malignant']))))]
} else {
pdata[, cell_type := factor(cell_type, levels = sort(unique(cell_type)))]
}
}
if('sample' %in% names(pdata)) {
if(!any(is.na(as.numeric(unique(pdata$sample))))) {
pdata[, sample := factor(as.character(sample), levels = sort(as.numeric(unique(sample))))]
} else pdata[, sample := factor(as.character(sample), levels = sort(as.character(unique(sample))))]
}
if('randomcoloR' %in% .packages(TRUE)) c(list(
title_tail = title_tail,
plots = slapply(
c('cell_type', 'sample')[c('cell_type', 'sample') %in% names(pdata)],
function(vn) ct_umap_plot(pdata, vn, colours = plot_colours[[vn]][levels(pdata[[vn]])],
legend_title = gsub('_', ' ', str_to_title(vn)))
)
)) else c(list(
title_tail = title_tail,
plots = slapply(
c('cell_type', 'sample')[c('cell_type', 'sample') %in% names(pdata)],
function(vn) ct_umap_plot(pdata, vn, legend_title = gsub('_', ' ', str_to_title(vn)))
)
))
})
if(all(sapply(out, is.null))) next
# A4 page is 210x297mm. Here, I'm allowing 20mm for the title and 15mm each for the "A" and "B" labels.
rmdlines <- c(
'---\n',
'title: ""\n',
'header-includes:\n',
' \\renewcommand{\\familydefault}{\\sfdefault}\n', # Indent is important but must use spaces, NOT tabs!
' \\pagenumbering{gobble}\n',
'geometry: margin=1cm\n',
'output: pdf_document\n',
'papersize: a4\n',
'---\n',
'\n',
'```{r setup, include = FALSE}\n',
'knitr::opts_chunk$set(echo = FALSE, warning = FALSE, error = FALSE, dev = "cairo_pdf")\n',
'```\n'
)
for(i in 1:length(out)) {
saveRDS(out[[i]]$plots, paste0('umap_plots_', i, '.rds'))
if(i > 1) rmdlines <- c(rmdlines, '\n\\newpage\n')
if(length(out[[i]]$plots) == 2) {
rmdlines <- c(
rmdlines,
'\n',
'### UMAP in ', out[[i]]$title_tail, '\n',
'\n',
'```{r}\n',
'plots <- readRDS("umap_plots_', i, '.rds")\n',
'```\n',
'\n',
'### **A**\n',
'\n',
'```{r fig.align = "center", fig.height = ', 130/25.4, ', fig.width = ', 180/25.4, ', out.width = "80%", out.height = "80%"}\n',
'plots$cell_type\n',
'```\n',
'\n',
'### **B**\n',
'\n',
'```{r fig.align = "center", fig.height = ', 130/25.4, ', fig.width = ', 180/25.4, ', out.width = "80%", out.height = "80%"}\n',
'plots$sample\n',
'```\n',
'\n',
'\\vspace*{\\fill}\n', # Aligns text with bottom of page
'\n',
'**A.** UMAP plot of single cells in ', out[[i]]$title_tail, ', after quality control. Cells are colored by cell type. **B.** ',
'UMAP plot as in A, with cells colored by sample.\n'
)
} else {
rmdlines <- c(
rmdlines,
'\n',
'### UMAP in ', out[[i]]$title_tail, '\n',
'\n',
'```{r}\n',
'plots <- readRDS("umap_plots_', i, '.rds")\n',
'```\n',
'\n',
'```{r fig.align = "center", fig.height = ', 130/25.4, ', fig.width = ', 180/25.4, ', out.width = "80%", out.height = "80%"}\n',
'plots[[1]]\n',
'```\n',
'\n',
'UMAP plot of single cells in ', out[[i]]$title_tail, ', after quality control. Cells are colored by ',
gsub('_', ' ', names(out[[i]]$plots)), '.\n'
)
}
}
out_con <- file('temp.Rmd')
writeLines(rmdlines, con = out_con, sep = '')
close(out_con)
rmarkdown::render('temp.Rmd', output_file = paste0('../data/study_plots/', gsub('/', '-', r[2]), '/', r[1], '/UMAP.pdf'))
file.remove('temp.Rmd')
for(i in 1:length(out)) file.remove(paste0('umap_plots_', i, '.rds'))
}
}