Single column heat map for TSS, genes appear out of order.

[Kenneth Lim]

Hello Groups,

I am using ngs.plot to show some transcription factor chip data, and the regions on my plot appear to be out of order? My understanding was that each row in the heat map represents the region around the TSS of a particular gene. The amount of red along each line represents the amount of enrichment at each point along the that region. The rows are ordered from top to bottom by most to least enrichment or most to least amount of red on the line.

The last part is where I am confused. My heat map looks like lines with more red are ranked below lines with less red. This gives my heat map a patchy look that I've never seen before (see attached).

CMD:

ngs.plot.r -G mm10 -R tss -C my_sample.bam -O my_sample_ngs

Based on my understanding of the plot, there shouldn't be any patchiness with a single bam as input. I've tried reinstalling ngs.plot and still get "patchiness".

I'm just would like an explanation for the patchiness as it doesn't match my understanding of how the heat map should look.

Thanks so much!