plot peak2gene heatmap vizualization question

[pseudacriscrucifer]

Hello,

How can I use plotBrowserTrack() to visualize chromatin accessibility surrounding my marker genes, sorted by samples that differ based on condition (experimental v. control)?

I have not had success doing this changing the useGroups parameter. GroupBy parameter is correct, as it is corresponds to the "Clusters2" parameter from the tutorial that is properly labeled cell type clusters following RNA-seq integration.

Running plotBrowserTrack() as shared immediately below performs properly, but I need to be able to produce and visualize these browser tracks at marker genes for both "Bx" and "Veh" conditions, as this mode offers chromatin accessible peaks for both Bx and Veh conditions.

p_bt_2Nov <- plotBrowserTrack( ArchRProj = project, region = NULL, groupBy = "Clusters2", useGroups = NULL, plotSummary = c("bulkTrack", "geneTrack"), sizes = c(10, 4), features = getPeakSet(project), loops = getCoAccessibility(project), geneSymbol = c("Apoe", "Tmem119", "Abca1"), useMatrix = NULL, log2Norm = TRUE, upstream = 50000, downstream = 50000, tileSize = 250, minCells = 25, normMethod = "ReadsInTSS", threads = getArchRThreads(), ylim = NULL, pal = NULL, baseSize = 7, scTileSize = 0.5, scCellsMax = 100, borderWidth = 0.4, tickWidth = 0.4, facetbaseSize = 7, geneAnnotation = getGeneAnnotation(project), title = "", verbose = TRUE, logFile = createLogFile("plotBrowserTrack") )

My archR project object is called 'project', and relevant information includes:

project
class: ArchRProject 
outputDirectory: /home/usr/Bexa/BxVehArchRProjOut 
samples(2): Bx Veh
sampleColData names(1): ArrowFiles
cellColData names(28): Sample TSSEnrichment ... ReadsInPeaks FRIP
numberOfCells(1): 61353
medianTSS(1): 21.772
medianFrags(1): 13657

project@sampleColData
DataFrame with 2 rows and 1 column
                ArrowFiles
               <character>
Bx  ./scRNAseq_analysis/..
Veh ./scRNAseq_analysis/..

project@sampleMetadata
List of length 2
names(2): Bx Veh

Would this be the correct function to accomplish browser track production of chromatin accessibility at marker genes separated by experimental condition?

Thank you.