suppressPackageStartupMessages({
library(scater)
library(SingleCellExperiment)
library(slingshot)
})
snr <- commandArgs()[8]
sample_num = paste0("sample", snr)
data.dir = "/nobackup/16tb_b/scRNA/10x_genomics/"
sample.dir = file.path(data.dir, snr)
plot.dir <- file.path(sample.dir, "plots")
log.file <- file.path(sample.dir, "slingshot.log")
sce <- readRDS(file.path(sample.dir, paste0("sample", snr, "_sce.rds")))
bp <- BiocParallel::registered()[[1]]
## 1. marker genes
cat("Run slingshot ...:\n", file=log.file)
# try: full and filter mat
# try: clusterLabels and celltype labels
reducedDims(sce)$PCA <- reducedDims(sce)$PCA[,1:10]
sce <- slingshot(sce, clusterLabels = "Cluster", reducedDim = "PCA", approx_points=200)
# annotate to sce
ind <- grep("slingPseudotime", colnames(colData(sce)), value=TRUE)
cat(paste0("\n\n Estimated trajectories: ", length(ind)),
file=log.file, append=TRUE)
pdf(file.path(plot.dir, "slingshot.pdf"))
for(n in ind) plotTSNE(sce, colour_by=n)
dev.off()
saveRDS(sce, file = file.path(sample.dir, paste0("sample", snr, "_sce.rds")))
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