SingleR-inc / SingleR

Clone of the Bioconductor repository for the SingleR package.
https://bioconductor.org/packages/devel/bioc/html/SingleR.html
GNU General Public License v3.0
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Fix color control of plotScoreHeatmap when 'normalize=TRUE' #259

Closed dtm2451 closed 5 months ago

dtm2451 commented 6 months ago

Per #197

Bug Fix: This PR ensures that when users supply their own color map to the plotScoreHeatmap() function, it will be used regardless of whether normalize was set to TRUE.

New Feature: Also gives users expanded control over their legend by newly allowing override of SingleR's default strategies for filling the pheatmap inputs breaks, legend_breaks, and legend_labels.

ToDo:

dtm2451 commented 5 months ago

Double-checked other pheatmap inputs that we explicitly touch in the function. All the ones already recorded as inputs are good now, but there 3 currently touched "siltently": breaks, legend_breaks, legend_labels.

If I remember correctly, the plan was to give all of these as explicit inputs so that they could be documented for the user, and I've done that in my last commit.

Also, I might need to rely on you @LTLA to get the updated man pages built. I'm having a bit of trouble getting a proper SingleR dev environment set up at the moment. (Bioconductor hosted devel docker image fails at installing Rcpp, so... can't install SingleR or SingleR deps.) Still working on a solution here, but I can't run R CMD CHECK, roxygen2::roxygenize(), or even test things locally in the meantime.

LTLA commented 5 months ago

LGTM, I just did some minor editing of the doc strings.

LTLA commented 5 months ago

I'm just going to merge and ignore the CI issues; can't do much about those.