Commit beb2a623 authored by Spencer Barnes's avatar Spencer Barnes
Browse files

modify diffmeth script

parent ff6be21a
Pipeline #7496 passed with stages
in 401 minutes and 40 seconds
......@@ -263,7 +263,7 @@ process diffMeth{
file diffmethDesign
output:
set file("*.txt"), file("*.pdf"), file("*html") into diffMethResults
set file("*.txt"), file("*.pdf"), file("*html"), file("*zip") into diffMethResults
file("version_r.txt") into diffMethVersions
script:
......@@ -273,6 +273,8 @@ process diffMeth{
R --version > version_r.txt
Rscript $baseDir/scripts/diff_meth.R -f $diffmethDesign -a $params.genome
zip -r lib.zip lib
"""
}
......
This diff is collapsed.
......@@ -35,7 +35,8 @@ if(!require("chromoMap")){
library(methylKit)
library(argparse)
library(htmltools)
library(chromoMap)
#library(chromoMap)
source("../../../workflow/scripts/chromoMap_modified.R")
# Create parser object
......@@ -139,11 +140,11 @@ write.table(chrom.data, file = paste0(unique(sapply(group.list,"[[",1))[1],"_v_"
row.names = FALSE, col.names = FALSE, sep = "\t", quote = FALSE)
#create map
c.map <- chromoMap(ch.files = genome.sizes, data.files = paste0(unique(sapply(group.list,"[[",1))[1],"_v_", unique(sapply(group.list,"[[",1))[2],"_chromo_data.txt"),
c.map <- chromoMap2(ch.files = genome.sizes, data.files = paste0(unique(sapply(group.list,"[[",1))[1],"_v_", unique(sapply(group.list,"[[",1))[2],"_chromo_data.txt"),
data_based_color_map = TRUE,
data_type = "numeric",
legend = TRUE, lg_y = 300,
data_colors = list("blue","white","red"))
legend = TRUE, lg_y = 300)#,
# data_colors = list("blue","white","red"))
save_html(c.map, file=paste0(unique(sapply(group.list,"[[",1))[1],"_v_",
unique(sapply(group.list,"[[",1))[2],"_chromomap.html"))
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