## ----knitr-options, echo=FALSE, message=FALSE, warning=FALSE, include = FALSE---- library(knitr) opts_chunk$set( collapse = TRUE, fig.align = 'center', fig.width = 6, fig.height = 5, dev = 'png', comment = "#>" ) ## ---- eval=FALSE-------------------------------------------------------------- # library(devtools) # devtools::install_github("QinglinMei/RCSL") ## ---- results="hide"---------------------------------------------------------- library(RCSL) library(SingleCellExperiment) library(ggplot2) library(igraph) library(umap) ## ----------------------------------------------------------------------------- head(ann) yan[1:3, 1:3] origData <- yan label <- ann$cell_type1 ## ---- cache=TRUE-------------------------------------------------------------- data <- log2(as.matrix(origData) + 1) gfData <- GenesFilter(data) ## ---- cache=TRUE-------------------------------------------------------------- resSimS <- SimS(gfData) ## ---- cache=TRUE-------------------------------------------------------------- Estimated_C <- EstClusters(resSimS$drData,resSimS$S) ## ---- cache=TRUE-------------------------------------------------------------- resBDSM <- BDSM(resSimS$S, Estimated_C) ## ---- cache=TRUE-------------------------------------------------------------- ARI_RCSL <- igraph::compare(resBDSM$y, label, method = "adjusted.rand") ## ---- cache=TRUE-------------------------------------------------------------- DataName <- "Yan" res_TrajecAnalysis <- TrajectoryAnalysis(gfData, resSimS$drData, resSimS$S, clustRes = resBDSM$y, TrueLabel = label, startPoint = 1, dataName = DataName) ## ---- cache=TRUE-------------------------------------------------------------- res_TrajecAnalysis$MSTPlot ## ---- cache=TRUE-------------------------------------------------------------- res_TrajecAnalysis$PseudoTimePlot ## ---- cache=TRUE-------------------------------------------------------------- res_TrajecAnalysis$TrajectoryPlot