peak2gene links specific clusters

[LacquerHed]

Im wondering how you can set code to get peak2gene loops only for specific clusters? I have the following and can see peaks from specific clusters but the loops extend to peaks not present in the field of view so wanted to limit both to one cluster. Thanks.

p <- plotBrowserTrack(
  ArchRProj = ArchR_subset_C5_13_14_integrated1, 
  groupBy = "Clusters2", 
  geneSymbol = markerGenes, 
  upstream = 60000,
  downstream = 60000,
  ylim = c(0,1),
  tileSize = 600,
  features = getMarkers(markersPeaks, cutOff = "FDR <= 0.1 & Log2FC >= 1", returnGR = TRUE)["PEC_0"],
  loops = getPeak2GeneLinks(ArchR_subset_C5_13_14_integrated1)
)

grid::grid.newpage()
grid::grid.draw(p$Itgav)

[rcorces]

you would need to subset the output of getPeak2GeneLinks() to only contain the loops you are interested in and then provide that to the loops argument

[LacquerHed]

I guess thats where Im getting stuck, not sure where in that output cluster information tied to specific loops is stored. Thanks.

[rcorces]

there are no "cluster-specific" loops per se. You could, for example, identify the cluster-specific peaks you are interested in and then only display loops with anchors overlappping those peaks.

[LacquerHed]

I am attempting the following to subset one cluster for peak2gene linkage analysis and getting this error:

idxSample <- BiocGenerics::which(Klf4_PEC_ArchR_subset_C5_13_14_integrated1$Clusters2 %in% "PEC_0")
cellsSample <- Klf4_PEC_ArchR_subset_C5_13_14_integrated1$cellNames[idxSample]
Klf4_PEC_ArchR_subset_C5_13_14_integrated1[cellsSample, ]

Klf4_PEC_ArchR_subset_C5_13_14_integrated1 <- addPeak2GeneLinks(
  ArchRProj = Klf4_PEC_ArchR_subset_C5_13_14_integrated1,
  reducedDims = "IterativeLSI"
)

p2g <- getPeak2GeneLinks(
  ArchRProj = Klf4_PEC_ArchR_subset_C5_13_14_integrated1,
  corCutOff = 0.45,
  resolution = 1,
  returnLoops = FALSE,
)

p2g
metadata(p2g)[[1]]

#set returnLoops = TRUE, then getPeak2GeneLinks() will return a loop track GRanges object that connects the peak and gene
p2g <- getPeak2GeneLinks(
  ArchRProj = Klf4_PEC_ArchR_subset_C5_13_14_integrated1,
  corCutOff = 0.45,
  resolution = .1,
  returnLoops = TRUE
)

Error in .validInput(input = start, name = "start", valid = c("integer")) : 
  Input value for 'start' is not a integer, (start = numeric) please supply valid input!
In addition: Warning message:
In min(abs(c(input%%1, input%%1 - 1)), na.rm = TRUE) :
  no non-missing arguments to min; returning Inf