Plotting functions for CNV data

Installation

Install from github:

git clone https://github.com/nriddiford/cnvPlotteR.git

Start an R session, and install package:

library(devtools)
install_github("nriddiford/cnvPlotteR")
library(cnvPlotteR)

Plot Control Freec normalised CNs

The function freecPlot will plot all CNs for for all chromosomes (if using a non-Drosophila genome the variables chroms and autosomes should be adjusted accordingly). Sub-clonal CNs are highlighted too.

chromosome_names <- c('2L', '2R', '3L', '3R', 'X', "Y")

file.names <- dir("data/freec", pattern = ".txt")

for (f in file.names){
  freecPlot(cnv_file=paste("data/freec/",f, sep=''), write=F, sex="XY", chroms=chromosome_names)
}

Other plotting functions are for CNV-Seq output

• Designed to read output from CNV-Seq, although should work for any coverage data with cols:

"chromosome" "start" - 1-based window start "end" - 1-based window end "test" - number of reads mapped in window in tumour sample "ref" - number of reads mapped in window in normal sample "position" - (end - start) +1 "log2" - log2 FC for tumour/normal reads per window

Example output from CNV-Seq:

"chromosome"    "start" "end"   "test"  "ref"   "position"      "log2"  "p.value"       "cnv"   "cnv.size"      "cnv.log2"      "cnv.p.value"
"X"     1       10000   50      74      5000    -0.292601981038923      2.85779196291872e-06    0       NA      NA      NA
"X"     5001    15000   50      72      10000   -0.253073616852285      4.12598434147092e-05    0       NA      NA      NA
"X"     10001   20000   2       2       15000   0.272995194815302       7.96882592007325e-06    0       NA      NA      NA
"X"     15001   25000   0       0       20000   NA      NA      0       NA      NA      NA
"X"     20001   30000   0       0       25000   NA      NA      0       NA      NA      NA
"X"     25001   35000   0       0       30000   NA      NA      0       NA      NA      NA
"X"     30001   40000   0       0       35000   NA      NA      0       NA      NA      NA

Plot all cnvs in specified directory for all chromosomes

• Currently assumes Drosophila genome, and excludes chroms 4 and Y for grid plot. Will look for .cnv files in 'data/' unless alternative path provided

allPlot(path = 'path/to/cnv_files/')

Plot single chromosome

• Will default to plotting X chromosome if chrom not specified

chromPlot(cnv_file = "data/test.window-10000.cnv")

• Plot all chroms for all files:

file.names <- dir("data/", pattern = ".cnv")

for (f in file.names){
  for (c in c("2L", "2R", "3L", "3R", "X")){
    chromPlot(chrom=c, cnv_file=paste("data/cnvs/",f, sep=''))
  }
}

Plot region for specified chromosome

• Will by default plot region around N on X if no to or from specified

 regionPlot(cnv_file="data/w500/test.window-500.cnv", from=3050000, to=3450000, chrom="X", ylim=c(-7,7), bp1=3129368,bp2=3352041, tick=100000, title="222Kb DEL on X")

Plot coverage for all '.count' files

• Use defaults: readLength = 100, windowSize = 50000

file.names <- dir("data/counts/", pattern = ".count")

for (f in file.names){
  plotCoverage(counts_file=paste("data/counts/",f, sep=''))
}

To do

• Allow user to control Y axis limits (for subtle CN changes)
• Build in depth plots
• Fix the ticks in Notch plots (show every 10kb?, start at round number)
• Clean up the function calls (i.e. chrom=NA -> chrom=X to set as default)