## ----echo = FALSE------------------------------------------------------------- library(knitr) ## ----------------------------------------------------------------------------- # Running slinghsot suppressPackageStartupMessages(library(slingshot)) data("slingshotExample") rd <- slingshotExample$rd colnames(rd) <- c("Dim1", "Dim2") cl <- slingshotExample$cl df <- data.frame(rd, "cl" = as.character(cl)) sds <- slingshot(rd, cl) ## ----------------------------------------------------------------------------- suppressPackageStartupMessages(library(ggplot2)) suppressPackageStartupMessages(library(dplyr)) # Plotting the results p <- ggplot(df, aes(x = Dim1, y = Dim2)) + geom_point(aes(fill = cl), col = "grey70", shape = 21) + theme_classic() p ## ----------------------------------------------------------------------------- curves <- slingCurves(sds, as.df = TRUE) p + geom_path(data = curves %>% arrange(Order), aes(group = Lineage)) ## ----------------------------------------------------------------------------- p + geom_path(data = curves %>% arrange(Order), aes(group = Lineage), size = 1.5) ## ----------------------------------------------------------------------------- p + geom_path(data = curves %>% arrange(Order), aes(group = Lineage, col = as.character(Lineage)), size = 1.5) ## ----------------------------------------------------------------------------- mst <- slingMST(sds, as.df = TRUE) ## ----------------------------------------------------------------------------- p + geom_point(data = mst, size = 4) ## ----------------------------------------------------------------------------- p + geom_point(data = mst, size = 4) + geom_path(data = mst %>% arrange(Order), aes(group = Lineage), size = 2) ## ----------------------------------------------------------------------------- suppressPackageStartupMessages(library(scater)) suppressPackageStartupMessages(library(SingleCellExperiment)) sce <- SingleCellExperiment(assays = list(counts = t(rd)), colData = df) reducedDim(sce, "Dim") <- rd p <- plotReducedDim(sce, dimred = "Dim", colour_by = "cl") p ## ----------------------------------------------------------------------------- curves <- slingCurves(sds, as.df = TRUE) %>% dplyr::rename("X" = "Dim1", "Y" = "Dim2") p + geom_path(data = curves %>% arrange(Order), aes(group = Lineage)) ## ----------------------------------------------------------------------------- mst <- slingMST(sds, as.df = TRUE) %>% dplyr::rename("X" = "Dim1", "Y" = "Dim2") p + geom_point(data = mst, size = 4) + geom_path(data = mst %>% arrange(Order), aes(group = Lineage), size = 2) ## ----------------------------------------------------------------------------- sessionInfo()