Custom signal range for plotBrowserTrack()

[RegnerM2015]

Hi @rcorces and @jgranja24

Is there a way to plot a custom signal range using the ReadsinTSS Norm method?

I would like to lower the default signal range so that I can more clearly see lower signal peaks.

Thanks!

[rcorces]

The ylim argument?

[RegnerM2015]

@rcorces

I have tried manipulating the ylim argument, but the browser track becomes blank. Does it matter that I am using ArchR 0.9.5?

plot <- plotBrowserTrack(atac,geneSymbol = "SOX9", groupBy = "predictedGroup_ArchR",
                         ylim=.5)

[rcorces]

I think there was a bug in .bulkTracks() which I think I fixed via
a861399
and
8caa716

You can update this in 0.9.5 on your end. That being said, dont use ylim=0.5, that is way too low for a quantile. start at 0.9.

If you could confirm that this fix works for you, I'll incorporate it into 1.0.2

[RegnerM2015]

a861399 works on my end!

Thanks so much for your help!

[rcorces]

For posterity, my changes mentioned above were not correct and actually broke the ArchRBrowser. The problem was actually with the plotBrowserTrack() function parameter documentation. I've corrected this in release_1.0.2 via 63e7883
Long story short, the syntax is ylim = c(0,0.9) rather than using a single value for ylim

This was in response to #1206

[RegnerM2015]

Thanks! I have since updated my workflows to the latest version of ArchR so I don't anticipate having these issues.