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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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TAD annotation colors #336

Closed mujahida87 closed 3 years ago

mujahida87 commented 3 years ago

Hi, I tried to color the TADs according to my TAD annotation (e.g. active, silent, PcG). But I can't see my given color in the output image. Can you please have a look at my input file, if the given format is correct? Than you

1) --version pyGenomeTracks 3.6, Python 2.7.5

2) my command: /apps/hicexplorer/3.6/bin/pyGenomeTracks --tracks tracks.ini --region X:6000000-9000000 --trackLabelFraction 0.2 --width 38 --dpi 130 -o plot.png

3) input my file > Screenshot 2021-04-26 at 11 31 24 4) output image> Screenshot 2021-04-26 at 11 34 21

lldelisle commented 3 years ago

Hi, I think you did not set the color of the TAD track: color = bed_rgb See https://pygenometracks.readthedocs.io/en/latest/content/examples.html#examples-with-multiple-options

mujahida87 commented 3 years ago

yes, it's sorted. Thank you much

lldelisle commented 3 years ago

I see that you also used the 5th field (score), if you want to use this field you need to use a colormap as a color: color = Reds