rose identifies super enhancers, how to output PDF files

Question

[shuailong]

Dear Professor: rose identifies super enhancers, how to output PDF files, its default output image is PNG

[Ram]

Dear Professor:

We are a community of volunteers, most of whom are not professors. You can just say "Hi".

Answer 1

[Ram]

I'm assuming this is the ROSE you're referring to: https://github.com/stjude/ROSE (you should be as specific as you can when you mention software by name)

The plotting code seems to be in R. Here's the line that starts the plotting logic: https://github.com/stjude/ROSE/blob/master/bin/ROSE_callSuper.R#L135

Change this:

plotFileName = paste(outFolder,enhancerName,'_Plot_points.png',sep='')
png(filename=plotFileName,height=600,width=600)

to

plotFileName = paste(outFolder,enhancerName,'_Plot_points.pdf',sep='')
pdf(file=plotFileName,height=600,width=600)

It'll be a little more work to make the output format parameterized but you could always implement it and add a Pull Request to the GitHub repository.

[shuailong]

Thank you for your answer.

[Ram]

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