The file format should look like this:
1 866642 921679 2 normal eg.txt
1 921679 982372 2 normal eg.txt
It is a tab separated .txt file with 6 columns without header. The information is as follows:
- Chromosome
- Startpoint of CN state
- Endpoint of CN state
- CNstate
- Meaning (loss, gain or normal)
- Original samplename
As the samplenames in the plot are generated from the filename, the filenames need to be chosen properly and must end with "_CNVs".
"D:/DIRECTORY"means you have to put the directory to the files / the working directory in here.- There is a function in the script that merges all files to one big dataframe.
sortedNames <- c("",""): Here you have to add all sample/filenames (without _CNVs) if you want a specific order, if not just remove the function and also the next one for the opposite order.- The filtering is set to exclude all CNVs smaller 500 bp, play a bit around with the numbers
- The output format here is a .pdf file. Depending on the number of samples, you have to play around a bit with the size:
pdf(file="outputname.pdf", width=8, height=5, pointsize=6, useDingbats=FALSE)and of course: add a filename.
reshape2 (version 1.4.3): Wickham, Hadley (2007): Reshaping Data with the reshape Package. In J. Stat. Soft. 21 (12).
ggplot2 (version 2.2.1): H. Wickham. ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag New York, 2016.
gtools (version 3.5.0): Gregory R. Warnes, Ben Bolker, and Thomas Lumley (2018): Various R Programming Tools.