Plot with log scale, high cnv

[jotanan98]

Hi,
Is there any way i could generate a manhattan plot using log scaling on the y axis? I am working with cancer cell and have really high cnv on some chromosome.

If its not possible, is there a way to output all the region that have more than 10X cnv? This way i could simply add a 'X' marker above the concerned chromosome.

Thank you for your time.

[suvakov]

Hi,
Sorry for delay. It is possible now (last commit). Two parameters should be set:

set rd_manhattan_log_scale
set rd_manhattan_range -5 5
manhattan

Units for range are based on Log2. Output should look like this (xkcd style):

Thanks

[jotanan98]

thanks!

[mtinti]

Hi, I was trying to get the plot in log scale as suggested, but my figure looks like this:

any suggestion, please?