[Q]can plotpup.py show log2FC

[BenxiaHu]

Hello,
I want to know whether plotpup.py can show log2FC between 2 Pileups?

Not sure whether what the --scale: Possible choices: log, linear (Whether to use linear or log scaling for mapping colours) mean.
I tried --scale, but it does not work

[efriman]

Hi BenxiaHu. The only built-in option is the natural logarithm, which you get by default or by "--scale log". If you want to plot the ratio between two pileups, you can simply add "--divide_pups" to the plotpup.py command.

[BenxiaHu]

plotpup.py --input_pups A_coolpuppy -o A_coolpuppy.pdf --plot_ticks --colnames 'A' --scale 'log'

So the scale is log(ratio), right？

however,
plotpup.py --input_pups A_coolpuppy -o A_coolpuppy.pdf --plot_ticks --colnames 'A' --scale 'linear' output a similar result

[efriman]

The log scale is the scale of the colormap, and depending on the values a linear scale will not lead to a very different result.