karchern

scale_color_manual does not support palette even though documentation suggests otherwise

1

Hi, I've just stumbled upon [issue 3182](https://github.com/tidyverse/ggplot2/issues/3182), having encountered exactly the same issue (briefly, the documentation of `scale_color_manual` suggests it should work with a `palette` (i.e. a function that returns...

Low cluster coverage

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I'm trying to use parsnp to infer core genes (and importantly, get rid of signal introduced by recombination in core genes) on around 1000 bins retrieved from metagenomes. The problem...

majority of input genomes get ignored

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Hi, I ran parsnp in the fasta-reference mode only (so no genbank file). I put more than 500 query genomes into a folder, but only 36 of them were actually...

parsnp for bins from metagenomic assembly

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Hello, I have a couple of hundreds of bins corresponding to strains of a bacterial species. Is it sensible to use parsnp to infer sites of recombination in core genes...

ENH: Include directionality of feature association in beeswarm plot

1

### Problem Description First of all, thanks for the idea and implementartion! We're adopting SHAP values in our model evaluations and find them very useful overall but struggle with the...