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Change sciprt for "chr"prefix chromosome #16

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Change sciprt for "chr"prefix chromosome #16

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ae62fe5
Update VisCap.R
leefall Nov 25, 2019
3da8d25
Update VisCap.R
leefall Nov 25, 2019
6216c6e
Update VisCap.R
leefall Dec 13, 2019
c6f1f34
Update VisCap.R
leefall Dec 13, 2019
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10 changes: 5 additions & 5 deletions VisCap.R
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Original file line number Diff line number Diff line change
Expand Up @@ -136,7 +136,7 @@ heatmap_by_chrom <- function(mat, analysis_name, ylimits, out_dir) {
pdf(file=paste(out_dir, "/", analysis_name, ".pdf", sep=""))

#Per-chromosome plots
chroms = c("all", 1:22,"X","Y", "MT", "M")
if(length(interval_lookup$chr[grep("chr",interval_lookup$chr)])!=0){chroms <- c("all",paste("chr",1:22,sep=""),"chrX","chrY", "chrMT", "chrM")}else{chroms = c("all", 1:22,"X","Y", "MT", "M")}
for(chr in chroms){
if(chr == "all") {
main_title <- "All Chromosomes"
Expand Down Expand Up @@ -255,7 +255,7 @@ call_cnvs <- function(nmat, ylimits, interval_lookup, threshold.min_exons, iqr_m
for(id in colnames(nmat_cnvs)) {
segs <- c()
segs.header <- c("Sample", "CNV", "Genome_start_interval", "Genome_end_interval", "Start_interval","End_interval", "Interval_count", "Min_log2ratio", "Median_log2ratio", "Max_log2ratio", "Loss_threshold", "Gain_threshold", "Batch_size")
chroms = c(1:22,"X","Y", "MT", "M")
if(length(interval_lookup$chr[grep("chr",interval_lookup$chr)])!=0){chroms <- c(paste("chr",1:22,sep=""),"chrX","chrY", "chrMT", "chrM")}else{chroms = c(1:22,"X","Y", "MT", "M")}
for(chr in chroms){
matches <- grep(paste("^",chr,":",sep=""), rownames(nmat))
if(length(matches) > 1) {
Expand Down Expand Up @@ -347,7 +347,7 @@ exon_plot_per_sample <- function(nmat, ylimits, interval_lookup, cnv_bplot_and_c

#Plot all intervals, then plot by chromosome
pdf(file=paste(out_dir, "/", name, ".plot.pdf", sep=""))
chroms <- c(".*", 1:22, "X", "Y")
if(length(interval_lookup$chr[grep("chr",interval_lookup$chr)])!=0){chroms <- c(".*",paste("chr",1:22,sep=""),"chrX","chrY")}else{chroms = c(".*", 1:22,"X","Y")}
for(chr in chroms) {
#Grep rownames with genome coordinates for desired chromosome, support chr1: and 1: formats
matches <- grep(paste("(^chr", chr, "|^", chr, "):", sep=""), rownames(nmat))
Expand Down Expand Up @@ -565,8 +565,8 @@ mat.all[which(mat.all==0)]=0.00001
# Read interval name files
interval_lookup <- load_interval_names(interval_list_dir, interval_file_pattern)

# Sort matrix by genome coordinates found in rownames
chroms <- c(1:22,"X","Y", "MT", "M")
# Sort matrix by genome coordinates found in rownames
if(length(interval_lookup$chr[grep("chr",interval_lookup$chr)])!=0){chroms <- c(paste("chr",1:22,sep=""),"chrX","chrY", "chrMT", "chrM")}else{chroms <- c(1:22,"X","Y", "MT", "M")}
chroms <- factor(chroms, levels=chroms, labels=chroms, ordered=TRUE)
coords <- matrix(unlist(strsplit(rownames(mat.all), ":|-")), ncol=3, byrow=TRUE, dimnames=list(rownames(mat.all)))
coords <- coords[order(match(coords[,1], chroms), as.numeric(coords[,2]), as.numeric(coords[,3])),]
Expand Down