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open2c / coolpuppy

A versatile tool to perform pile-up analysis on Hi-C data in .cool format.
MIT License
77 stars 11 forks source link

[Q]only two huge squares in the final plot #120

Closed jiangshan529 closed 1 year ago

jiangshan529 commented 1 year ago

Hi, I run the code to plot a local pileup figure(TAD boundaries at TF peak center): " coolpup.py aa.cool TF_center_nochr.bed --outname aa_1kb_250pad.txt --flank 250 --n_proc 8 --local --clr_weight_name "" plotpup.py --input_pups aa_1kb_250pad.txt --not_symmetric --output Figure5A.pdf " However, the plot looks like this, what should I do image

Phlya commented 1 year ago

You need to increase the flank, in the new version it is in bp.

jiangshan529 commented 1 year ago

You need to increase the flank, in the new version it is in bp.

Thanks, that helps! However, now the plot does not show values for the bar, how can I change it? Thanks!

image

efriman commented 1 year ago

This is a bug that sometimes happens but I haven't been able to reliably reproduce when using --not_symmetric. For now, either set --vmin and --vmax manually or use symmetric scale. I'll look into it