Skip to content
Permalink
07d492c88e
Switch branches/tags

Name already in use

A tag already exists with the provided branch name. Many Git commands accept both tag and branch names, so creating this branch may cause unexpected behavior. Are you sure you want to create this branch?

master_project_JLU2018/bin/2.2_motif_estimation/png_to_pdf.R

Go to file
 
 
Cannot retrieve contributors at this time
94 lines (70 sloc) 7.63 KB
Raw Blame
#!/usr/bin/env Rscript
if (!require(optparse)) install.packages("optparse"); library(optparse)
if (!require(png)) install.packages("png"); library(png)
if (!require(grid)) install.packages("grid"); library(grid)
if (!require(gridExtra)) install.packages("gridExtra"); library(gridExtra)
option_list <- list(
make_option(opt_str = c("-i", "--png_new"), default = NULL, help = "List of png paths separated by \',\'", metavar = "character"),
make_option(opt_str = c("-p", "--png_old"), default = NULL, help = "List of png paths separated by \',\'", metavar = "character"),
make_option(opt_str = c("-f", "--index"), default = NULL, help = "Path to index file", metavar = "character")
)
opt_parser <- OptionParser(option_list = option_list,
description = "Generating a PDF from multiple png files",
epilogue = "Author: Rene Wiegandt <Rene.Wiegandt@mpi-bn.mpg.de>")
opt <- parse_args(opt_parser)
#' Generating a PDF from multiple png files.
#'
#' @parameter png_new <string> List of png paths separated by ,
#' @parameter png_old <string> List of png paths separated by ,
#' @parameter cluster_ids <string> List of IDs separated by ,
#' @parameter new_id <int> New Cluster ID
#'
#' @author Rene Wiegandt
#' @contact rene.wiegandt(at)mpi-bn.mpg.de
png_to_pdf <- function(png_top, png_list, cluster_ids, new_id, out = "cluster.pdf"){
#png_top <- "G://Rene.Wiegandt/10_Master/tmp/test_pipeline_11_3_19/2.2_motif_estimation/03_motif_cluster/04_glam2/Cluster_0/logo1.png,G://Rene.Wiegandt/10_Master/tmp/test_pipeline_11_3_19/2.2_motif_estimation/03_motif_cluster/04_glam2/Cluster_0/logo2.png,G://Rene.Wiegandt/10_Master/tmp/test_pipeline_11_3_19/2.2_motif_estimation/03_motif_cluster/04_glam2/Cluster_0/logo3.png"
#png_list <- "G://Rene.Wiegandt/10_Master/tmp/test_pipeline_11_3_19/2.2_motif_estimation/02_glam2/buenrostro50k_chr1_fp_cluster_0/logo1.png,G://Rene.Wiegandt/10_Master/tmp/test_pipeline_11_3_19/2.2_motif_estimation/02_glam2/buenrostro50k_chr1_fp_cluster_0/logo2.png,G://Rene.Wiegandt/10_Master/tmp/test_pipeline_11_3_19/2.2_motif_estimation/02_glam2/buenrostro50k_chr1_fp_cluster_0/logo3.png,G://Rene.Wiegandt/10_Master/tmp/test_pipeline_11_3_19/2.2_motif_estimation/02_glam2/buenrostro50k_chr1_fp_cluster_1/logo1.png,G://Rene.Wiegandt/10_Master/tmp/test_pipeline_11_3_19/2.2_motif_estimation/02_glam2/buenrostro50k_chr1_fp_cluster_1/logo2.png,G://Rene.Wiegandt/10_Master/tmp/test_pipeline_11_3_19/2.2_motif_estimation/02_glam2/buenrostro50k_chr1_fp_cluster_1/logo3.png,G://Rene.Wiegandt/10_Master/tmp/test_pipeline_11_3_19/2.2_motif_estimation/02_glam2/buenrostro50k_chr1_fp_cluster_0/logo1.png,G://Rene.Wiegandt/10_Master/tmp/test_pipeline_11_3_19/2.2_motif_estimation/02_glam2/buenrostro50k_chr1_fp_cluster_0/logo2.png,G://Rene.Wiegandt/10_Master/tmp/test_pipeline_11_3_19/2.2_motif_estimation/02_glam2/buenrostro50k_chr1_fp_cluster_0/logo3.png,G://Rene.Wiegandt/10_Master/tmp/test_pipeline_11_3_19/2.2_motif_estimation/02_glam2/buenrostro50k_chr1_fp_cluster_1/logo1.png,G://Rene.Wiegandt/10_Master/tmp/test_pipeline_11_3_19/2.2_motif_estimation/02_glam2/buenrostro50k_chr1_fp_cluster_1/logo2.png,G://Rene.Wiegandt/10_Master/tmp/test_pipeline_11_3_19/2.2_motif_estimation/02_glam2/buenrostro50k_chr1_fp_cluster_1/logo3.png,G://Rene.Wiegandt/10_Master/tmp/test_pipeline_11_3_19/2.2_motif_estimation/02_glam2/buenrostro50k_chr1_fp_cluster_0/logo1.png,G://Rene.Wiegandt/10_Master/tmp/test_pipeline_11_3_19/2.2_motif_estimation/02_glam2/buenrostro50k_chr1_fp_cluster_0/logo2.png,G://Rene.Wiegandt/10_Master/tmp/test_pipeline_11_3_19/2.2_motif_estimation/02_glam2/buenrostro50k_chr1_fp_cluster_0/logo3.png,G://Rene.Wiegandt/10_Master/tmp/test_pipeline_11_3_19/2.2_motif_estimation/02_glam2/buenrostro50k_chr1_fp_cluster_1/logo1.png,G://Rene.Wiegandt/10_Master/tmp/test_pipeline_11_3_19/2.2_motif_estimation/02_glam2/buenrostro50k_chr1_fp_cluster_1/logo2.png,G://Rene.Wiegandt/10_Master/tmp/test_pipeline_11_3_19/2.2_motif_estimation/02_glam2/buenrostro50k_chr1_fp_cluster_1/logo3.png,G://Rene.Wiegandt/10_Master/tmp/test_pipeline_11_3_19/2.2_motif_estimation/02_glam2/buenrostro50k_chr1_fp_cluster_0/logo1.png,G://Rene.Wiegandt/10_Master/tmp/test_pipeline_11_3_19/2.2_motif_estimation/02_glam2/buenrostro50k_chr1_fp_cluster_0/logo2.png,G://Rene.Wiegandt/10_Master/tmp/test_pipeline_11_3_19/2.2_motif_estimation/02_glam2/buenrostro50k_chr1_fp_cluster_0/logo3.png,G://Rene.Wiegandt/10_Master/tmp/test_pipeline_11_3_19/2.2_motif_estimation/02_glam2/buenrostro50k_chr1_fp_cluster_1/logo1.png,G://Rene.Wiegandt/10_Master/tmp/test_pipeline_11_3_19/2.2_motif_estimation/02_glam2/buenrostro50k_chr1_fp_cluster_1/logo2.png,G://Rene.Wiegandt/10_Master/tmp/test_pipeline_11_3_19/2.2_motif_estimation/02_glam2/buenrostro50k_chr1_fp_cluster_1/logo3.png,G://Rene.Wiegandt/10_Master/tmp/test_pipeline_11_3_19/2.2_motif_estimation/02_glam2/buenrostro50k_chr1_fp_cluster_0/logo1.png,G://Rene.Wiegandt/10_Master/tmp/test_pipeline_11_3_19/2.2_motif_estimation/02_glam2/buenrostro50k_chr1_fp_cluster_0/logo2.png,G://Rene.Wiegandt/10_Master/tmp/test_pipeline_11_3_19/2.2_motif_estimation/02_glam2/buenrostro50k_chr1_fp_cluster_0/logo3.png,G://Rene.Wiegandt/10_Master/tmp/test_pipeline_11_3_19/2.2_motif_estimation/02_glam2/buenrostro50k_chr1_fp_cluster_1/logo1.png,G://Rene.Wiegandt/10_Master/tmp/test_pipeline_11_3_19/2.2_motif_estimation/02_glam2/buenrostro50k_chr1_fp_cluster_1/logo2.png,G://Rene.Wiegandt/10_Master/tmp/test_pipeline_11_3_19/2.2_motif_estimation/02_glam2/buenrostro50k_chr1_fp_cluster_1/logo3.png"
#cluster_ids <- c(1,2,3,4,5,6,7,8,9,10)
top_split <- unlist(strsplit(png_top, ","))
png_split <- unlist(strsplit(png_list, ","))
cluster_list <- unlist(strsplit(cluster_ids, ","))
top_grob <- lapply(top_split,function(p){rasterGrob(readPNG(p),interpolate = FALSE)})
grobs <- lapply(png_split,function(p){rasterGrob(readPNG(p),interpolate = FALSE)})
split_grobs <- split(grobs, rep(1:ceiling(length(grobs)/3), each = 3)[1:length(grobs)])
rows <- lapply(seq(1,length(split_grobs)), function(sg){
arrangeGrob(grobs = split_grobs[[sg]], top = textGrob(paste0("Cluster ",cluster_list[sg]),gp = gpar(fontsize = 20,font = 3)), ncol = 3)
})
split_rows <- split(rows, rep(1:ceiling(length(rows)/4), each = 4)[1:length(rows)])
pdf(out,width = 17, height = 11)
grid.arrange(grobs = top_grob, nrow = 3, top = textGrob(paste0("New Cluster ",new_id),gp = gpar(fontsize = 30,font = 3)))
lapply(split_rows, function(r){
grid.arrange(grobs = r, nrow = 4, top = textGrob("Generated from...",gp = gpar(fontsize = 30,font = 3)))
})
dev.off()
}
#### index_file <- "G://Rene.Wiegandt/10_Master/tmp/test_pipeline_11_3_19/2.2_motif_estimation/03_motif_cluster/03_merged_fasta/cluster.txt"
#' Parsing index file.
#'
#' @parameter index_file Path to index file.
#'
#' @author Rene Wiegandt
#' @contact rene.wiegandt(at)mpi-bn.mpg.de
get_index <- function(index_file){
f <- data.table::fread(index_file, header = F)
index <- f[,c(2,8)]
index$V8 <- strsplit(index$V8,",")
return(index[unlist(lapply(index$V8, function(v){ifelse(length(v) > 1, TRUE, FALSE)}))])
}
png_to_pdf_set_up <- function(png_top, png_list, index_file){
index <- get_index(index_file)
t <- lapply(seq(nrow(index)), function(i){
new_id <- index[i,1]
cluster_ids <- index[i,2]
out <- paste0("Summary_cluster_", new_id, ".pdf")
png_to_pdf(png_top = ,png_list = ,cluster_ids = cluster_ids, new_id = new_id, out = out )
})
}
# run function merge_similar with given parameteres if not in interactive context (e.g. run from shell)
if (!interactive()) {
png_to_pdf_set_up(opt$png_new, opt$png_old , opt$index)
}