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master_project_JLU2018/bin/2.2_motif_estimation/png_to_pdf.R

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#!/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$V8, function(v){ifelse(length(v) > 1, TRUE, FALSE)}))])
}
@TODO
png_to_pdf_set_up <- function(png_top, png_list, index_file){
index <- get_index(index_file)
t <- lapply(seq(nrow(index)), function(i){
new_id <- index[i,1]
cluster_ids <- index[i,2]
out <- paste0("Summary_cluster_", new_id, ".pdf")
#regex_png <- paste0("*_cluster_", new_id , "/logo${NUM}.png") #????
png_to_pdf(png_top = "TODO" ,png_list = "TODO" ,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)
}