Merge pull request #3 from loosolab/hic_dev

Hic dev

RLIB/cis_matrix_body_multi.R

@@ -47,7 +47,7 @@ require(plyr, quietly = TRUE)
 require(RColorBrewer, quietly = TRUE)
 require(gridExtra, quietly = TRUE)
 require(grid, quietly = TRUE)
-require(ggplot2 ,quietly = TRUE)
+##require(ggplot2 ,quietly = TRUE)
 require(ggpmisc, quietly = TRUE)
 if ( !(require("ggbio")) ) {
   biocLite("ggbio")
@@ -145,7 +145,7 @@ if(colour_range[2] == 0){
 #}
 
 wh <- GenomicRanges::GRanges(region[["chr"]], IRanges::IRanges(as.integer(region[["start"]]),as.integer(region[["end"]])))
-tset <- ggbio::autoplot(txdb , which = wh, genome.axis = FALSE, names.expr = "tx_name")
+tset <- ggbio::autoplot(txdb , which = wh, genome.axis = FALSE, names.expr = "gene_id")
 p2 <- tset@ggplot
 
 
@@ -154,15 +154,16 @@ palette <- c(
   rgb(0,0,255,maxColorValue=255),
   rgb(152,20,18,maxColorValue=255),
   rgb(240,48,0,maxColorValue=255),
-  rgb(255,188,39,maxColorValue=255))
+  rgb(255,188,39,maxColorValue=255),
+  rgb(124,252,0,maxColorValue=255))
 
 # triangle plot
 message(paste("Constructing plot"))
 p <- ggplot2::ggplot()
 p <- p + geom_polygon(aes(x=x, y=y, group=group), fill="black", data=rotated_bg)
 if(add_borders_to_elements){
   p <- p + geom_polygon(aes(x=x, y=y, group=group, fill=signal, colour=signal), data=rotated_data, size=0.2)
-  p <- p + scale_colour_gradientn(limits=colour_range, colours=palette, na.value = "green")
+  p <- p + scale_colour_gradientn(limits=colour_range, colours=palette, na.value = "green", guide = "colourbar")
 } else {
   p <- p + geom_polygon(aes(x=x, y=y, group=group, fill=signal), data=rotated_data)
 }

bin/xaxis_scaling.R

@@ -0,0 +1,19 @@
+#!/usr/bin/env Rscript
+args <- commandArgs(trailingOnly=TRUE)
+
+path <- args[1]
+start <- as.numeric(args[2])
+end <- as.numeric(args[3])
+out <- args[4] #"./out.txt"
+
+tad <- data.table::fread(path, header = TRUE , sep = ' ')
+xaxis <- tad[,1]
+xmax <- max(xaxis)
+
+newxaxis <- lapply(xaxis, function(x){
+  new_x <- (((end - start) * x) / xmax) + start
+})
+
+tad[,1] <- round(unlist(newxaxis[1]))
+
+data.table::fwrite(tad, file = out, col.names = TRUE, sep = ' ', quote = FALSE)

envtoucan.yaml

@@ -0,0 +1,10 @@
+name: envtoucan
+channels:
+  - bioconda
+  - conda-forge
+  - defaults
+dependencies:
+  - bwa=0.7.15
+  - samtools=1.3.1
+  - bedtools=2.27.1
+  - bowtie2=2.3.3.1

nextflow.config

@@ -1,35 +1,21 @@
 
 //Paths to dependencies
 env {
-	path_bowtie2 = "/mnt/software/x86_64/packages/bowtie2/2.3.3.1/" //Path to bowtie2
 	path_python = "/mnt/software/x86_64/packages/python/2.7.8-anaconda-5.1.0-stretch/bin"		//Path to python
-	path_bwa = "/mnt/software/x86_64/packages/bwa/0.7.12/bin"		//Path to bwa
-	path_samtools = "/mnt/software/x86_64/packages/samtools/1.3.1/bin"	//Path to samtools
-	path_bedtools = "/mnt/software/x86_64/packages/bedtools/2.27.1/bin"	//Path to bedtools
+	path_R = "/mnt/software/x86_64/packages/r/3.4.4-stretch-local/bin" //Path to R
 
-	path_bin = "/mnt/workspace1/rene.wiegandt/NextFlow/script/THCPipe"		// Path to T2C analysis scripts
-	path_working = "/mnt/workspace1/rene.wiegandt/NextFlow/script/THCPipe"		//Path to directory where files are stored. If restriction maps are already existing put them in folder 01_restriction_maps inside this working_dir
+	path_bin = "/mnt/workspace1/rene.wiegandt/NextFlow/script/TOuCAN"		// Path to T2C analysis scripts
+	path_working = "/mnt/workspace1/rene.wiegandt/NextFlow/script/TOuCAN"		//Path to directory where files are stored. If restriction maps are already existing put them in folder 01_restriction_maps inside this working_dir
 
 	path_genome = "/mnt/workspace1/rene.wiegandt/NextFlow/script/THCPipe/index_bwa/GRCm38.p5.genome_whitelist.fa" 		// Path to full genome in fasta format + basis name of index [e.g. GRCm38.p5.genome_whitelist.fa]
 	path_gtf = "/mnt/agnerds/Rene.Wiegandt/fromMario/gencode.vM15.annotation.gtf"
 
 	path_T2C_restriction_maps = "${path_working}/01_restriction_maps"		//If empty restriction maps are generated [typically: path_working + /01_restriction_maps/]. If empty files are generated
-	//path_bam_files = "/mnt/workspace1/rene.wiegandt/NextFlow/script/THCPipe/temp/"  //Path to alingment files. If empty files are generated
-
-	uropa_feature = "" // "String,String,String,..."
-	uropa_anchor = "" // "String,String,String,..."
-	uropa_dist_1 = 1000
-	uropa_dist_2 = 1000
-	uropa_strand = "" // single argument "String"
-	uropa_direction = "any_direction" // "String,String,String,..."
-	uropa_filter_attr = "" // "String,String,String,..."
-	uropa_attr_value = "" // "String,String,String,..."
-	uropa_show_attr = "gene_id,gene_type,gene_name,level,transcript_type,transcript_support_level" // "String,String,String,..."
 
 }
 
 params {
-	sample_extension = "_R[12]_001"//"_R[12]_001" // regex for sample extension [e.g "_R[12]_001" or "_R[12]"]
+	sample_extension = "_R[12]_001" // regex for sample extension [e.g "_R[12]_001" or "_R[12]"]
 
 	// Enzyme Information
 	// -------------------------------------------
@@ -40,8 +26,8 @@ params {
 
 	// Minor fixed parameters for BWA and SAMtools
 	// -------------------------------------------
-	bwa_T2C_options = "-t 4" // bwa aln
-	sort_options = "--threads 4"
+	bwa_T2C_options = "-t 16" // bwa aln
+	sort_options = "--threads 16"
 	library_label = "capture"
 	platform_label = "ILLUMINA"
 	center_label = "ECB"
@@ -55,9 +41,19 @@ params {
 
 	//Parameter for HiC matrix
 	//--------------------------------------------
-	hicBuildMatrix_options = "--threads 4 --inputBufferSize 100000"
-	bwa_HiC_options = "" // bwa mem
+	hicBuildMatrix_options = "--threads 16 --inputBufferSize 100000"
+	bwa_HiC_options = "-t 4" // bwa mem
 
+	//Parameter for uropa configuration
+	uropa_feature = "" // "String,String,String,..."
+	uropa_anchor = "" // "String,String,String,..."
+	uropa_dist_1 = 1000
+	uropa_dist_2 = 1000
+	uropa_strand = "" // single argument "String"
+	uropa_direction = "any_direction" // "String,String,String,..."
+	uropa_filter_attr = "" // "String,String,String,..."
+	uropa_attr_value = "" // "String,String,String,..."
+	uropa_show_attr = "gene_id,gene_type,gene_name,level,transcript_type,transcript_support_level" // "String,String,String,..."
 
 }
 

uropa.yaml

@@ -0,0 +1,8 @@
+name: uropa
+
+channels:
+  - bioconda
+  - conda-forge
+
+dependencies:
+  - uropa