What are those black lines in my heatmap?
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8 months ago
grx0326 • 0

I have been using deeptools plotHeatmap to generate heatmap around TSS regions from my chip-seq data.
However there are black lines in my heatmap and I don`t know what those lines stand for.
Here is my code:
plotHeatmap -m [prefix]matrix.gz -o [prefix]normalized.png --boxAroundHeatmaps no --colorMap bwr --heatmapHeight 15 --heatmapWidth 3 --whatToShow 'heatmap and colorbar' & And here is what I got:
enter image description here

Any ideas are appreciated

deeptools heatmap • 629 views
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Entering edit mode
8 months ago

They're missing data. You can change the color if you like.

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you mean change the black line into other color´╝čI am not sure how to achieve that

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It's the --missingDataColor option, see the online help page for more information: https://deeptools.readthedocs.io/en/develop/content/tools/plotHeatmap.html

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