Hi, I'm using ngsplot to generate a heatmap for ChIP-seq coverage. However, I would like to replot the heatmap myself with the underlying data provided by ngsplot.
I'm a bit confused about the scaling though. The heatmap generated by ngsplot has a scale of (0, 0.9) whereas the max value of the hm data provided by the program goes to 2.5. Is there a subset of data (outliers) that ngsplot ignores during the generation of its plots?
which command are you using and did you check the help section/documentation of that function? Most likely, there's some pruning of extreme values so that the dynamic range is not dominated by outliers with very high or very low numbers, but there may also be some z-score normalization or the like going on.
To follow up on this, this is what the
plotheat
function seems to do under the hood:Code from here. Disclaimer: I've never used that package so there may be additional intricacies.
I'm looking at the code, but I'm not able to tell exactly parameter is used as the cutoff limit. Could you shed some light on this?
The function I'm using within the program:
https://github.com/shenlab-sinai/ngsplot/blob/develop/bin/ngs.plot.r
what's the command you're typing?
cut-off parameter: flood.q