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deeptools / pyGenomeTracks

python module to plot beautiful and highly customizable genome browser tracks
GNU General Public License v3.0
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Missing y-axis scale on hicPlotTADs #79

Closed StephenRicher closed 5 years ago

StephenRicher commented 5 years ago

Hi,

I am making great use of this tool but am having trouble with plotting a scale bar on the HiC matrix generated via hicPlotTADs.

My figure looks the same as one of your test images at: https://github.com/deeptools/HiCExplorer/blob/master/hicexplorer/test/test_data/hicPlotTADs/pygenometracks.png

The colour scale bar is present but no numbers are there. I can't find the .ini file associated with the above test data plot but I was wondering if there was a setting in the configuration file that is causing these to not be plotted? As in the above figure all my other tracks plot the scales correctly.

Thanks, Stephen

vivekbhr commented 5 years ago

@StephenRicher are you able to reproduce this issue with pyGenomeTracks? If yes. please let us know the version number, config file and an example output.

StephenRicher commented 5 years ago

Hi,

Yep I have the same issue - I've attached a basic config file and test output below. I am using pyGenomeTracks 3.0.

Thanks, Stephen

test

tracks.txt

vivekbhr commented 5 years ago

Yes this looks like a known matplotlib issue. The labels were missing for ticks when you use log1p with certain matplotlib versions. I think updating your matplotlib would help

kimj50 commented 5 years ago

hi, I also ran into a similar problem. hicexplorer or pygenometrack doesn't show the tickmarks. I am currently using: pygenometracks v3.0, matplotlib v3.0.3. track: [x-axis] where = top

[hic matrix] file = /scratch/kimj50/elegans/matrix_normalize/N2_2017_emb_sum_5kb_correct_normalize.h5 title = test depth = 1000000 transform = log

test.pdf

lldelisle commented 5 years ago

Hi, I also have the same issue with pyGenomeTracks 3.0 with matplotlib v3.1.1 but also v3.0.3, and v3.0.1...

lldelisle commented 5 years ago

This is now solved since v3.1.