plotGeneCount {tradeSeq} | R Documentation |
Plot the gene in reduced dimension space
plotGeneCount(curve, counts = NULL, gene = NULL, clusters = NULL, models = NULL, title = NULL)
curve |
The output from a lineage computation |
counts |
the count matrix. |
gene |
The name of gene for which you want to plot the count or the row number of that gene in the count matrix. Alternatively, one can specify the cluster arguments |
clusters |
The assignation of each cell to a cluster. Used to color the
plot. Either |
models |
the list of GAMs, typically the output from
|
title |
Title for the plot. |
If both gene
and clusters
arguments are supplied, the
plot will be colored according to gene count level.
A ggplot
object
set.seed(97) library(slingshot) data(crv, package="tradeSeq") data(countMatrix, package="tradeSeq") rd <- slingshot::reducedDim(crv) cl <- kmeans(rd, centers = 7)$cluster lin <- slingshot::getLineages(rd, clusterLabels = cl, start.clus = 4) crv <- slingshot::getCurves(lin) counts <- as.matrix(countMatrix) gamList <- fitGAM(counts = counts, pseudotime = slingPseudotime(crv, na = FALSE), cellWeights = slingCurveWeights(crv)) plotGeneCount(crv, counts, gene = "Mpo")