## ----echo = FALSE------------------------------------------------------------- library(knitr) ## ----------------------------------------------------------------------------- library(slingshot) library(traviz) data(crv, package = "traviz") class(crv) rd <- slingReducedDim(crv) cl <- apply(slingClusterLabels(crv),1, function(x) which(x==1)) ## Only visualize the trajectory plot(crv) ## Visualize the trajectory on top of cells in reduced space plot(rd, pch=16, col=cl+1, cex=2/3) lines(crv, col="black", lwd=3) ## Visualizing trajectory and clusters using plotGeneCount plotGeneCount(crv, clusters=cl) ## ----------------------------------------------------------------------------- data(counts, package="traviz") plotGeneCount(crv, counts, gene = "Mpo") ## ----------------------------------------------------------------------------- plotExpression(counts=counts, sds=crv, gene="Car1") ## ----------------------------------------------------------------------------- data(sce, package="traviz") plotSmoothers(models = sce, counts = counts, gene = "Elane") ## ----------------------------------------------------------------------------- sessionInfo()