PercentageFeatureSet doesn't always work when specifying assay.

[maxim-h]

I've been trying to run PercentageFeatureSet on an object that already has multiple assays, with default one being integrated.

I do the following, but it doesn't work:

> PercentageFeatureSet(object = seurat, pattern = "^RP[LS]", assay = "RNA")
NULL

Pretty sure it's because PercentageFeatureSet searches for counts layers, but doesn't specify which assay to look for layers in.

seurat/R/utilities.R

Lines 1173 to 1174 in c54e57d

	layers <- Layers(object = object, search = "counts")
	for (i in seq_along(along.with = layers)) {

So, since integrated assay doesn't have a counts layer nothing works.

My guess is that just pushing the assay parameter down to Layers call should fix this.

[igrabski]

Thanks for bringing this to our attention! This indeed seems like a bug, and we will look into it. In the meantime, a workaround is to specify the DefaultAssay of your object as RNA (or whichever contains the counts layer you would like to use).