Try resolving dependency of BuenRTools (9387aca3) · Commits · github_fork / PRINT

analyses/BMMC/QC.R

+8 −7

Original line number	Diff line number	Diff line
		@@ -2,6 +2,7 @@
		if (Sys.getenv("RSTUDIO") == "1"){
		setwd(dirname(rstudioapi::getActiveDocumentContext()$path))
		}
		source("../../code/utils.R")
		library(ggplot2)
		library(Seurat)
		library(GenomicRanges)
		@@ -66,7 +67,7 @@ dev.off()

		norm <- 100
		flank <- 2000
		TSS <- sort(sortSeqlevels(BuenRTools::hg38TSSRanges))
		TSS <- sort(sortSeqlevels(FigR::hg38TSSRanges))
		chr <- paste0(seqnames(TSS))
		chr <- gtools::mixedsort(intersect(chr, paste0(seqnames(TSS))))
		splitTSS <- split(GenomicRanges::resize(TSS,1,"start"), seqnames(TSS))[chr]
		@@ -134,7 +135,7 @@ markers <- c("CD34", "TCL1A", "CD79A", "CD4", "CD3D", "GIMAP5", "CREM",
		"HBA2", "GNG11")

		scRNACounts <- scRNASeurat@assays$RNA@counts
		scRNACounts <- BuenRTools::centerCounts(scRNACounts, chunkSize = 1e5)
		scRNACounts <- centerCounts(scRNACounts, chunkSize = 1e5)

		pdf("../../data/BMMC/plots/QC/RNADotPlot.pdf",
		width = 7, height = 5.5)
		@@ -155,13 +156,13 @@ scATACSE <- SummarizedExperiment::SummarizedExperiment(
		)

		# Calculate gene scores
		geneScores <- BuenRTools::getGeneScoresFromPeaks(scATACSE,
		geneScores <- getGeneScoresFromPeaks(scATACSE,
		genome = "hg38",
		TSSwindow = 10000,
		getWeightsOnly = FALSE)

		# Normalize gene scores
		geneScores <- BuenRTools::centerCounts(geneScores, chunkSize = 1e5)
		geneScores <- centerCounts(geneScores, chunkSize = 1e5)

		pdf("../../data/BMMC/plots/QC/ATACDotPlot.pdf",
		width = 7, height = 5.5)

+6 −6

Original line number	Diff line number	Diff line
		@@ -77,13 +77,13 @@ pseudobulkCenters$group <- pseudobulkNames
		#########################################

		# Calculate gene scores
		geneScores <- BuenRTools::getGeneScoresFromPeaks(scATACSE,
		geneScores <- getGeneScoresFromPeaks(scATACSE,
		genome = "mm10",
		TSSwindow = 10000,
		getWeightsOnly = FALSE)

		# Normalize gene scores
		geneScores <- BuenRTools::centerCounts(geneScores, chunkSize = 1e4)
		geneScores <- centerCounts(geneScores, chunkSize = 1e4)

		# Marker genes to plot
		markers <- c("Cd3d", "Gata1", "Cd79a", "Selp",
		@@ -164,7 +164,7 @@ dev.off()
		scRNAMtx <- scRNASeurat@assays$RNA@counts

		# Normalize RNA data
		scRNAMtx <- BuenRTools::centerCounts(scRNAMtx, chunkSize = 5000)
		scRNAMtx <- centerCounts(scRNAMtx, chunkSize = 5000)

		# Smooth the gene scores of marker genes
		KNN <- FNN::get.knn(scATACSeurat@reductions$lsi@cell.embeddings[colnames(scRNASeurat), 2:20], k = 500)$nn.index

+6 −6

Original line number	Diff line number	Diff line
		@@ -2,7 +2,7 @@
		if (Sys.getenv("RSTUDIO") == "1"){
		setwd(dirname(rstudioapi::getActiveDocumentContext()$path))
		}

		source("../../code/utils.R")
		library(Seurat)
		library(Signac)
		library(SummarizedExperiment)
		@@ -159,13 +159,13 @@ dev.off()
		#################

		# Calculate gene scores
		geneScores <- BuenRTools::getGeneScoresFromPeaks(scATACSE,
		geneScores <- getGeneScoresFromPeaks(scATACSE,
		genome = "mm10",
		TSSwindow = 10000,
		getWeightsOnly = FALSE)

		# Normalize gene scores
		geneScores <- BuenRTools::centerCounts(geneScores)
		geneScores <- centerCounts(geneScores)

		# Calculate gene score of cluster markers
		seuratClusters <- scATACSeurat$seurat_clusters

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