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jernst98 / ChromHMM

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discrepancy between X_Y_overlap.png and X_Y_overlap.txt #41

Closed keksundso closed 2 years ago

keksundso commented 2 years ago

Hi, I wanted to redo the overlap plot based on the .txt file output. However, the values do not correlate with the plot. E.g. for state 11 the enrichment seems to be higher on TSS2kb compared to the TSS (see image left). However, according to the txt file, the genome value is 30 and the gene 11 (se image middle).

Dividing each column by its base value and scaling it all to one (genome column is treated differently) creates a fairly similar plot, however its not identical (e.g the above described difference persists).

Screenshot from 2021-11-12 13-30-52

So it seems I am either misinterpreting the plot or the table, but I am not sure which one.

jernst98 commented 2 years ago

ChromHMM by default colors each column on its own color scale. It appears you are using a uniform color scale. OverlapEnrichment gives the option to use a uniform color scale with the flag '-uniformscale'.

-Jason

keksundso commented 2 years ago

thank you very much! That makes sense