I want to subset a cluster from archr project by running clustree. on this specific cluster and put it back to the archproject.

subset cluster9

idxSample <- BiocGenerics::which(project_Peaks_MACS2_RES0.9$Clusters.res_RNA0.9 %in% "C9") cellsSample <- project_Peaks_MACS2_RES0.9$cellNames[idxSample] CLUSTER9 <- project_Peaks_MACS2_RES0.9[cellsSample, ]

CLUSTER9 <- addIterativeLSI(

ArchRProj = CLUSTER9,

#useMatrix = "GeneExpressionMatrix", 
#depthCol = "Gex_nUMI",
#varFeatures = 2500,
#firstSelection = "variable",
#binarize = FALSE,
#name = "LSI_RNA_C9", force = TRUE

)

CLUSTER9 <- addUMAP(ArchRProj = CLUSTER9, reducedDims = "LSI_RNA", name = "UMAP_RNA", force = TRUE)

CLUSTERING

for(i in seq(0,0.9,0.1)){ CLUSTER9 <- addClusters(input = CLUSTER9, reducedDims = "LSI_RNA",method = "Seurat", force = TRUE, name = paste("Clusters.res_RNA_C9",i,sep=""),resolution = i, verbose = FALSE) }

CLUSTER9 <- addUMAP(ArchRProj = CLUSTER9, reducedDims = "LSI_RNA", name = "UMAP_RNA_C9", force = TRUE)

tmp.clustree.datatable<-as.data.frame(CLUSTER9@cellColData) clustree(tmp.clustree.datatable, prefix="Clusters.res_RNA_C9")

nb of cluster found with the new clustering of this subset

I can not use properly mapLabels labelNew <- c(CLUSTER9$Clusters.res_RNA_C90.4) labelNew

remapClust <- c( "C1" = "C9a", "C2" = "C9b", "C3" = "C9c")

remapClust <- remapClust[names(remapClust) %in% labelNew]

labelNew2 <- mapLabels(labelNew, oldLabels = names(remapClust), newLabels = remapClust) labelNew2

CLUSTER9$newclust_9 <- labelNew2 CLUSTER9df <- getCellColData(CLUSTER9, select = c("newclust_9", "Clusters.res_RNA_C90.4")) CLUSTER9df$cellNames <- rownames(CLUSTER9df)

df <- getCellColData(project_Peaks_MACS2_RES0.9, select = "Clusters.res_RNA0.9") df$cellNames <- rownames(df)

all <- merge(df, CLUSTER9df, by = "cellNames", all = TRUE)

all$cluster <- ifelse(all$Clusters.res_RNA0.9 == "C9", all$newclust_9, all$Clusters.res_RNA0.9) table(all$cluster, all$Clusters.res_RNA0.9)

length(project_Peaks_MACS2_RES0.9$cellNames)

project_Peaks_MACS2_RES0.9$new_cluster_sub <-all$cluster

project_Peaks_MACS2_RES0.9$new_cluster_sub <- all$cluster

table(project_Peaks_MACS2_RES0.9$new_cluster_sub, project_Peaks_MACS2_RES0.9$Clusters.res_RNA0.9)

before subdivision

after subdivision

Hi @A-legac45! Thanks for using ArchR! Please make sure that your post belongs in the Issues section. Only bugs and error reports belong in the Issues section. Usage questions and feature requests should be posted in the Discussions section, not in Issues.
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GreenleafLab / ArchR

mapLabels function #2081