## ----echo=FALSE, results="hide", message=FALSE-------------------------------- require(knitr) library(BiocStyle) opts_chunk$set(error=FALSE, message=FALSE, warning=FALSE) ## ----------------------------------------------------------------------------- library(scRNAseq) sce <- HermannSpermatogenesisData() sce ## ----------------------------------------------------------------------------- sce <- sce[, 1:500] ## ----------------------------------------------------------------------------- library(scuttle) sce <- logNormCounts(sce, assay.type=1) library(scran) dec <- modelGeneVar(sce) top.hvgs <- getTopHVGs(dec, n=2000) ## ----------------------------------------------------------------------------- library(velociraptor) velo.out <- scvelo(sce, subset.row=top.hvgs, assay.X="spliced") velo.out ## ----------------------------------------------------------------------------- library(scater) set.seed(100) sce <- runPCA(sce, subset_row=top.hvgs) sce <- runTSNE(sce, dimred="PCA") sce$velocity_pseudotime <- velo.out$velocity_pseudotime plotTSNE(sce, colour_by="velocity_pseudotime") ## ----------------------------------------------------------------------------- embedded <- embedVelocity(reducedDim(sce, "TSNE"), velo.out) grid.df <- gridVectors(sce, embedded, use.dimred = "TSNE") library(ggplot2) plotTSNE(sce, colour_by="velocity_pseudotime") + geom_segment(data=grid.df, mapping=aes(x=start.1, y=start.2, xend=end.1, yend=end.2, colour=NULL), arrow=arrow(length=unit(0.05, "inches"))) ## ----------------------------------------------------------------------------- # Only setting assay.X= for the initial AnnData creation, # it is not actually used in any further steps. velo.out2 <- scvelo(sce, assay.X=1, subset.row=top.hvgs, use.dimred="PCA") velo.out2 ## ----------------------------------------------------------------------------- velo.out3 <- scvelo(sce, assay.X=1, use.theirs=TRUE) velo.out3 ## ----------------------------------------------------------------------------- velo.out4 <- scvelo(sce, assay.X=1, subset.row=top.hvgs, scvelo.params=list(recover_dynamics=list(max_iter=20))) velo.out4 ## ----------------------------------------------------------------------------- sessionInfo()