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LieberInstitute / spatialLIBD

Code for the spatialLIBD R/Bioconductor package and shiny app
http://LieberInstitute.github.io/spatialLIBD/
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Check default shiny app color code #32

Closed lcolladotor closed 2 years ago

lcolladotor commented 2 years ago

For some reason some two level factor variables, like spe$discard <- factor(c("TRUE", "FALSE")) are not being properly displayed in the shiny apps. They work well with the vis_clus*() functions. We noticed this in the Visium IF AD project with @shkwon17.

lcolladotor commented 2 years ago

I'm now thinking about adding an option to choose what color palette to use for the clusters. Though that wouldn't allow users to choose specific colors for specific variables.

I'm also thinking of search for the cluster name in the colData(spe) and add a _colors suffix. If that variable exists, then use that as the default color.

Anyways, this is going to involve a bit more effort than what I have time for today. I'm just leaving some notes for myself.