## ----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