x and y limits for plotCorrelation scatter plot

[dpryan79]

Instead of just a --maxRange, it'd be better to offer x and y axis limits.

[dpryan79]

This is now in develop.

[Xiaofei-git]

Could we set xRange and yRange at the same time? I will get an error if I want to set both of them as their own range.

$ plotCorrelation -in *.npz --corMethod pearson --skipZeros --xRange 0 2000 --yRange 0 2000 --plotTitle "Endosperm_Lai" --whatToPlot scatterplot -o *.png --outFileCorMatrix *.tab

Traceback (most recent call last):
File "**something/bin/plotCorrelation", line 12, in
main(args)
File "**something/Python/2.7.14/lib/python2.7/site-packages/deeptools/plotCorrelation.py", line 241, in main
log1p=args.log1p)
File "**something/Python/2.7.14/lib/python2.7/site-packages/deeptools/correlation.py", line 536, in plot_scatter
ax.set_ylim(min_yvalue, min(yRange, ax.get_ylim()[1]))
ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()

[Xiaofei-git]

Also, do you think is it possible to plot based on the normalized read counts within a bin because every sample is different, e.g. library size?

[dpryan79]

I have a PR to fix the error you ran into. Regarding your second question, if you create normalized bigWig files (using RPGC in bamCoverage) and use those with multiBamSummary then the results will be properly normalized.

[Xiaofei-git]

I am sorry I did not follow you for the first answer. What do you mean by "PR"?

[dpryan79]

PR is short for a "pull request" on github. It's now been merged and will appear in the next release.

[Xiaofei-git]

So, that is mean for the current version 3.1.1, I can't set x-range and y-range differently, am I right? Thanks!

[Xiaofei-git]

I mean set them respectively.

[dpryan79]

Correct, that's a bug in the current version. I'll release 3.1.2 when I'm back in the office on Monday.

[Xiaofei-git]

Thanks a lot!

…

On Thu, Aug 16, 2018 at 5:52 PM Devon Ryan ***@***.***> wrote: Correct, that's a bug in the current version. I'll release 3.1.2 when I'm back in the office on Monday. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#709 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AV1ZeTCHvL3MyVBYS9puwLJomXzE9zgtks5uRemGgaJpZM4UAB7-> .

[Xiaofei-git]

For the normalization, you said " if you create normalized bigWig files (using RPGC in bamCoverage) and use those with multiBamSummary then the results will be properly normalized". But, after generating the bigWig files, how can I pass them to multiBamSummary because "multiBamSummary bins" take bam files not bw format?

[dpryan79]

Try multiBigwigSummary instead.

[Xiaofei-git]

Thanks!

…

On Tue, Aug 21, 2018 at 3:41 PM Devon Ryan ***@***.***> wrote: Try multiBigwigSummary instead. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#709 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AV1ZeY5P-_1fbPrnxC5lIu875M8S_jk5ks5uTGJSgaJpZM4UAB7-> .