color.by argument does not always work

[toobiwankenobi]

gs <- list(Bcells = c("MS4A1", "CD79B", "CD79A", "IGH1", "IGH2"),
           Tcells = c("CD3E", "CD3D", "CD3G", "CD7","CD8A"))
            
pbmc <- SeuratObject::pbmc_small |>
runEscape(gene.sets = gs, min.size = NULL)

pbmc$RNA_snn_res.1

geyserEnrichment(pbmc, assay = "escape",
                gene.set = "Tcells",
                group.by = "groups", color.by = "RNA_snn_res.1")

> Error in geom_jitter(width = 0.25, size = 1.5, alpha = 0.6, na.rm = TRUE) : 
  
ℹ Error occurred in the 1st layer.
Caused by error in `.data[["RNA_snn_res.1"]]`:
! Column `RNA_snn_res.1` not found in `.data`.

The color.by argument from functions such as ridgeEnrichment() or geyserEnrichment() only works if this argument is identical to other arguments such as facet.by, group.by. The color.by information is not pulled by the utils function .prepData() and is thus not available.

The argument description for color.by says that Any other metadata or column present in the data is also accepted.

I suggested a fix in my fork. If you think its worth to fix it, i can create a pull request.

[ncborcherding]

Yes absolutely, this is a bug!!