What are those black lines in my heatmap?
1
0
Entering edit mode
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 dont 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:

Any ideas are appreciated

deeptools heatmap • 629 views
1
Entering edit mode
8 months ago

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

0
Entering edit mode

you mean change the black line into other color？I am not sure how to achieve that

0
Entering edit mode

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