## ----knitr-options, echo=FALSE, message=FALSE, warning=FALSE, include = FALSE---- knitr::opts_chunk$set(tidy = FALSE, cache = FALSE, dev = "png", message = FALSE, error = FALSE, warning = TRUE) ## ----eval=FALSE--------------------------------------------------------------- # library(devtools) # devtools::install_github("QinglinMei/RCSL") ## ----results="hide"----------------------------------------------------------- library(RCSL) library(SingleCellExperiment) library(ggplot2) library(igraph) library(umap) ## ----------------------------------------------------------------------------- data(yan, package = "RCSL") head(ann) yan[1:3, 1:3] origData <- yan label <- ann$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