hicPlotMatrix "--region 1:10000000-50000000" option is abnormal

[JiaoLaboratory]

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• [ ] Paste the full HiCExplorer command that produces the issue below (ignore if you simply spotted the issue in the code/documentation).

• [ ] Paste the output printed on screen from the command that produces the issue below (ignore if you simply spotted the issue in the code/documentation). Hi, I want to draw heatmap as below: my version: hicInfo 3.7.2 Python 3.7.12

hicConvertFormat -m ../inter_30.hic --inputFormat hic --outputFormat cool -o matrix.cool -resolutions 100000

hicPlotMatrix -m matrix_100000.cool -o matrix_100000.cool_chr1.png --clearMaskedBins --log1p --region 1

While when i use the --region option: hicPlotMatrix -m matrix_100000.cool -o matrix_100000.cool_chr1_10M_50M.png --clearMaskedBins --log1p --region 1:10000000-50000000

the map looks logged . could you give me some advice? what happend?

[lldelisle]

Hi, It seems to be a bug between --region and --clearMaskedBins. Can you try without --clearMaskedBins? Unfortunately we are lacking man power to address this issue. Is plotting triangle instead of square possible for you? If yes, please, use pyGenomeTracks, I think we don't have this bug.