This is a test version of Biostars. For the public version, visit https://www.biostars.org.
What are those black lines in my heatmap?

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
• 4,775 views • link
updated by Devon Ryan Devon Ryan • written by grx0326 • grx0326

1 answer

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

• 0 views • link
written by Devon Ryan Devon Ryan

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

• 0 views • link
written by grx0326 • grx0326

Log in to answer this question.

More posts like this