Adaptations to simplify making kmer/motif plots

fmicompbio / monaLisa

binned motif enrichment analysis and visualisation

https://fmicompbio.github.io/monaLisa/

GNU General Public License v3.0

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Adaptations to simplify making kmer/motif plots #44

Closed csoneson closed 3 years ago

csoneson commented 3 years ago

Opening this PR now to simplify comments, but with the understanding that we'll discuss the calculation of the Pearson residuals (esp. the pseudofrac) and adapt unit tests accordingly before merging.

mbstadler commented 3 years ago

I think the content of this PR is quite important (calculation of Pearson residual also happens in the motif-based analysis and is not restricted to the k-mer based analysis), and should also make it into master, as soon as possible. Let's discuss how we can achieve this, so it does not get left out from our submission to BioC.

mbstadler commented 3 years ago

closing this PR - all suggested changes have been added in the meantime to the kmers_to_motifs branch