Fix GroupCorrelation and GroupCorrelationPlot for Seurat V5 compatibility

[joesphbeller]

Discussed in issue #9483

Problem

In spatial_vignette.Rmd, GroupCorrelation() and GroupCorrelationPlot() would both generate the following error:

"Error in object[[assay]][] <- grp.cors: object of type 'S4' is not subsettable"

This is because the correlation was being stored in metafeatures, which is no longer an element of the assay in V5.

Solution

Insert 2 try() statements to make it compatible for previous and most recent versions of Seurat

[dcollins15]

@joesphbeller. thank you for taking the time and effort to translate your solution into a PR 🙌

I was not sure if this would cause any other functions that depend on GroupCorrelation or GroupCorrelationPlot to fail

AFAIK the blast radius for these two methods should be pretty small. In any case, your solution works well 🎉 That said, the fix could be refined further, so I’ve suggested a couple of improvements.

Thanks again!

[dcollins15]

Suggested change

	try(data <- object[[assay]]@meta.data[, c(feature.group, cor)], silent=T)
	try(data <- object[[assay]]@meta.features[, c(feature.group, cor)], silent=T)
	object[[assay]] <- object[[assay]][[c(feature.group, cor)]]

[dcollins15]

Suggested change

	try(object[[assay]]@meta.data <- grp.cors, silent = T)
	try(object[[assay]]@meta.features <- grp.cors, silent = T)
	object[[assay]] <- AddMetaData(object[[assay]], grp.cors)