Ordering of SpatialDimPlot Function, clarification and help

[alexwskh]

Hello, and thanks in advance for any help.

I am working with spatial data and trying to showcase some potential interactions by using the SpatialDimPlot function. There are three lists I'm working with... The first is a list of cells from one of the clusters, the second is a list of cells expressing two GOI, and the third is overlap between the first two lists.

Since this is just for visuals, I am trying to use the order of operations to just paint over the previous group as needed. I can confirm that the order matters, as if I put the second list of cells after the third in the function, it does not include that group (presumably because the next list of cells to be highlight completely overrides the former).

My problem is that function is not using the colors in the order provided... It's a minor issue, but I want to make sure I understand how and when elements are used.

cell_lists <- c(cluster2, doublepos, clus2doublepos) 
names(cell_lists) <- c("cluster2", "doublepos", "cluster2+doublepos" )

SpatialDimPlot(nb, cells.highlight = cell_lists, cols.highlight = c("green","red", "orange", "grey"))

So the expected behaviour is that cluster2 will be green, doublepos will be red, cluster2+doublepos will be orange, and unselected will be grey. Instead, doublepos is orange while cluster2+doublepos is red. Where is my understanding failing?

Thanks again.