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SCENIC_CART/SCENIC_CART_HM.R

+library(Seurat)
+library(devtools)
+library(loomR)
+library(SCopeLoomR)
+library(AUCell)
+library(SCENIC)
+library(dplyr)
+library(KernSmooth)
+library(RColorBrewer)
+library(plotly)
+library(BiocParallel)
+library(grid)
+library(ComplexHeatmap)
+library(data.table)
+library(openxlsx)
+
+wdir <- "./SCENIC_CART"
+
+scenicLoomPath <- file.path(paste(wdir, "Full_CART.from_tsv.loom", sep = "/"))
+motifEnrichmentFile <- file.path(paste(wdir, "Full_CART.adjacences.tsv", sep = "/"))
+
+loom <- open_loom(scenicLoomPath)
+# Read information from loom file:
+regulons_incidMat <- get_regulons(loom, column.attr.name = 'Regulons')
+regulons <- regulonsToGeneLists(regulons_incidMat)
+regulonAUC <- get_regulons_AUC(loom, column.attr.name = 'RegulonsAUC')
+regulonAucThresholds <- get_regulon_thresholds(loom)
+embeddings <- get_embeddings(loom)
+close_loom(loom)
+
+# Get metadata info
+cellClusters <- read.xlsx(xlsxFile = paste(wdir, "Full_CART_metadata.xlsx", sep = "/"), rowNames = T)
+
+### Fig6 B - SCENIC CART Heatmap ###
+selectedResolution <- "PROP.Condition"
+# Split the cells by cluster:
+cellsPerCluster <- split(rownames(cellClusters), cellClusters[,selectedResolution]) 
+regulonAUC <- regulonAUC[onlyNonDuplicatedExtended(rownames(regulonAUC)),]
+# Calculate average expression:
+regulonActivity_byCellType <- sapply(cellsPerCluster, function(cells) rowMeans(getAUC(regulonAUC)[,cells]))
+# Save regulon activity
+write.xlsx(x = list("RegulonActivity" = regulonActivity_byCellType), rowNames = T,
+           file = paste(wdir, "Full_CART_HM_regulonActivity.xlsx", sep = "/"))
+
+# Scale expression:
+regulonActivity_byCellType_Scaled <- t(scale(t(regulonActivity_byCellType), center = T, scale=T))
+
+# plot:
+gg_index <- which(rownames(regulonActivity_byCellType_Scaled) %in%
+                      c("Jund(+)","Foxo1(+)","Junb(+)","Klf2(+)","Fos(+)","Irf7(+)","Stat1(+)","Stat5b(+)","Klf9(+)","Irf4(+)","Jun(+)",
+                        "Stat5a(+)","Nfkb1(+)","Fosb(+)","Ikzf1(+)","Tfdp2(+)","Myc(+)","Irf5(+)","Bcl3(+)","Stat2(+)","Irf9(+)",
+                        "Nelfe(+)","Zscan29(+)","Zfp454(+)","Zic1(+)","Thap11(+)","Batf3(+)","Myb(+)","Tbx21(+)","Foxp1(+)","Eomes(+)"))
+gg_lab <- rownames(regulonActivity_byCellType_Scaled)[gg_index]
+hm_aanot <- rowAnnotation(link = anno_mark(at = gg_index, labels = gg_lab, labels_gp = gpar(fontsize = 10)))
+
+options(repr.plot.width = 8, repr.plot.height = 10)
+png(file = paste(wdir, "Full_CART_HM.png", sep = "/"))
+draw(ComplexHeatmap::Heatmap(matrix = regulonActivity_byCellType_Scaled,
+                             name = "Regulon activity",
+                             column_dend_side = "bottom",
+                             column_names_side = "top",
+                             column_names_rot = 0,
+                             show_row_names = FALSE,
+                             right_annotation = hm_aanot)) # row font size
+dev.off()
+