## ----message=F, warning=F, results=F------------------------------------------ library(scRNAseq) lung <- ZilionisLungData() immune <- lung$Used & lung$used_in_NSCLC_immune lung <- lung[,immune] lung <- lung[,1:5000] exp.mat <- Matrix::Matrix(counts(lung),sparse = TRUE) colnames(exp.mat) <- paste0(colnames(exp.mat), seq(1,ncol(exp.mat))) ## ----------------------------------------------------------------------------- signatures <- list( Tcell = c("CD3D","CD3E","CD3G","CD2","TRAC"), Myeloid = c("CD14","LYZ","CSF1R","FCER1G","SPI1","LCK-"), NK = c("KLRD1","NCR1","NKG7","CD3D-","CD3E-"), Plasma_cell = c("MZB1","DERL3","CD19-") ) ## ----message=F, warning=F----------------------------------------------------- library(UCell) library(SingleCellExperiment) sce <- SingleCellExperiment(list(counts=exp.mat)) sce <- ScoreSignatures_UCell(sce, features=signatures, assay = 'counts', name=NULL) altExp(sce, 'UCell') ## ----message=F, warning=F----------------------------------------------------- library(scater) library(patchwork) #PCA sce <- logNormCounts(sce) sce <- runPCA(sce, scale=TRUE, ncomponents=10) #UMAP set.seed(1234) sce <- runUMAP(sce, dimred="PCA") ## ----fig.width=7, fig.height=5, dpi=60---------------------------------------- pll <- lapply(names(signatures), function(x) { plotUMAP(sce, colour_by = x, by_exprs_values = "UCell", point_size=0.2) + theme(aspect.ratio = 1) }) wrap_plots(pll) ## ----------------------------------------------------------------------------- sce <- SmoothKNN(sce, signature.names = names(signatures), reduction="PCA") ## ----fig.wide=TRUE, dpi=60---------------------------------------------------- a <- plotUMAP(sce, colour_by="Myeloid", by_exprs_values="UCell", point_size=0.2) + ggtitle("UCell") + theme(aspect.ratio = 1) b <- plotUMAP(sce, colour_by="Myeloid_kNN", by_exprs_values="UCell_kNN", point_size=0.2) + ggtitle("Smoothed UCell") + theme(aspect.ratio = 1) a | b ## ----------------------------------------------------------------------------- sessionInfo()