search

ibiem-master / community

Discussion, Q&A, everything you want to say, formatted nicely
0 stars 0 forks source link

plotting lefse results #22

Open YiweiDuan opened 4 years ago

YiweiDuan commented 4 years ago

Are there any way to customize the plots lefse generates (with labels)? The autogenerated plots doesn't have labels and are of low resolution.

Any help would be appreciated!

granek commented 4 years ago

I would recommend doing this in R. Lefse's main job is to do biomarker discovery. The plots that lefse generates are convenient for a quick look, but if you want more control over the plots R is a better tool for the job. You should be able to this with phyloseq/ggplot2 using the relative abundance phyloseq object.

If you want to do something like this, I think that you can just prune taxa to the one you are interested, then do a facet plot.
It might be helpful to look at the figures and code here.

With ggplot2 you have lots of control over the resolution at which figures are generated (and saving as PDF would give you infinite resolution).

Try to figure this out and post back if you have problems.