Plot peakMatrix in embedding

[Zepeng-Mu]

Hi, I'm wondering if there is a way to plot a peak using plotEmbedding, like what we do with genes when using GeneScoreMatrix. Right now I cannot plot using peakMatrix because getFeatures() returns NULL. Thanks!!

[rcorces]

Yes - I've come across this before (#308 (comment))

Im not sure what the original rationale was for not having a name in PeakMatrix and whether there will be unforeseen downstream consequences. I'm also not sure what the ideal "name" of a peak should be.

For what its worth, you can get around this. For example:

ps <- projHeme5@peakSet
ps$name <- paste0(seqnames(ps),"_peak",ps$idx)
projHeme5@peakSet <- ps
projHeme5 <- addPeakMatrix(ArchRProj = projHeme5, force = TRUE, threads = 16)
plotEmbedding(
  ArchRProj = projHeme5,
  colorBy = "PeakMatrix",
  name = c("chr1_peak300"),
  embedding = "UMAP",
  quantCut = c(0.01, 0.95),
  imputeWeights = getImputeWeights(ArchRProj = projHeme5),
  rastr = TRUE,
  plotAs = "points"
)

For something more stable - I've added a line to addPeakSet() which should automatically add a name column to new peak sets.
2dfc240 in dev_peakName.
This works for me on dev_peakName. Let me know if it solves your problem.

ps <- projHeme5@peakSet
ps$name <- NULL
projHeme5 <- addPeakSet(ArchRProj = projHeme5, peakSet = ps, force = TRUE)
projHeme5 <- addPeakMatrix(ArchRProj = projHeme5, force = TRUE)
plotEmbedding(
  ArchRProj = projHeme5,
  colorBy = "PeakMatrix",
  name = c("chr1_peak300"),
  embedding = "UMAP",
  quantCut = c(0.01, 0.95),
  imputeWeights = getImputeWeights(ArchRProj = projHeme5),
  rastr = TRUE,
  plotAs = "points"
)

[Zepeng-Mu]

Thanks a lot! The first solution should work for me. Since I also use the peaks in other tools, I've been defining my own peak names, so I might just keep using my own names for now.