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mrvollger / StainedGlass

Make colorful identity heatmaps of genomic sequence
https://mrvollger.github.io/StainedGlass/
MIT License
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heatmap figure #35

Closed shehongbing closed 5 months ago

shehongbing commented 7 months ago

Hi, I get a figure, however, it is more like a dot plot. Is this my window (2000 kb) too small? Do you have any suggestions.

THX

Best wishes, Hongbing

chr1_false

mrvollger commented 5 months ago

StainedGlass will produce dot-plot-like figures if you have sequence that is e.g. a segmental duplication rather than a centromere array. This is effectively controlled by the window size parameters. If the size of the repeat unit (looks like >100kbp here) is much greater than the window size, it will appear like a dot-plot (which I think is accurate in this case).