Aaron Lun

I have no idea. This all works fine for me: ```r library(scRNAseq) test

No idea. `sc_data` doesn't even exist in the **SingleR** codebase AFAICT.

Depends on the gene annotation in your test samples. **SingleR** starts by taking the intersection of genes in the test and training datasets. After all, there's little point drawing inferences...

Hm. That cryptic error message is usually a symptom of a child job being killed. On my HPC, I often see this when I run out of memory somewhere, the...

@dtm2451 can you have a look at this?

Right... yeah, I guess we should at least respond to the user-supplied `color` when `normalize=TRUE`, and it's on the user to make sure they choose a sensible color scale. In...

@anoronh4 Funny you say that, because - thanks to the efforts of @j-andrews7 - the latest version of **SingleR** has Cell Ontology mappings returned for all labels in `ImmGenData()`. This...

@vjcitn: - I will add the `common_classes` example to the **SingleR** vignette. - I don't recall us discussing `subset_descendents`? - I wonder what would be an easy interface for users...

Right. Having poked around, I think `onto_plot2` may be close to what we need to close this issue. To restate the problem; the user has a bunch of terms near...

Having tried this, I don't think it's reasonable to expect people to poke through the plot: ```r library(ontoProc) library(ontologyPlot) library(SingleR) cl