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Old 06-20-2016, 09:47 AM   #1
ajsn6c
Junior Member
 
Location: columbia, missouri

Join Date: Oct 2015
Posts: 7
Default CummeRbund, extracting only one chromosome

So I'm new to R and want to create a scatterplot with cummeRbund that has only chr8 plots.

>pdf(file="practice_8.pdf")
> csScatter(genes(cuff_data), 'S1', 'S2')
> dev.off()

I feel like there's a line of code I'm missing to specify a chromosome.
I've also tried a different way; when I only did tophat and cuffdiff for chr8 reads, my graph in cummeRbund had x and y axis labeled as 10, 1000 etc on one axis and then 1e1, 1e3 etc on the other. I want both axis to be 10, 1000 etc, not mixed. Any help is appreciated.

Thank you!

Last edited by ajsn6c; 06-21-2016 at 04:43 PM.
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