plotGenePseudotime: Plot Gene Expression by Pseudotime

In slingshot: Tools for ordering single-cell sequencing

Description

Show the gene expression pattern for an individual gene along lineages inferred by slingshot.

Usage

plotGenePseudotime(data, ...)

## S4 method for signature 'SlingshotDataSet'
plotGenePseudotime(data, gene, exprs, loess = TRUE, loessCI = TRUE, ...)

## S4 method for signature 'SingleCellExperiment'
plotGenePseudotime(data, gene, exprs, loess = TRUE, loessCI = TRUE, ...)

Arguments

data	an object containing slingshot output, either a SlingshotDataSet or a SingleCellExperiment object.
...	additional parameters to be passed to plot.
gene	the gene to be plotted. If exprs is provided, this may be either the gene name or its row index in exprs. Otherwise, this is assumed to be a vector of scaled expression values.
exprs	the genes-by-samples matrix of scaled expression values (log counts or normalized log counts).
loess	logical, whether to include a loess fit in each plot (default is TRUE).
loessCI	logical, whether to include a confidence band around the loess curve (default is TRUE).

Value

returns NULL.

Examples

data("slingshotExample")
rd <- slingshotExample$rd
cl <- slingshotExample$cl
sds <- slingshot(rd, cl, start.clus = "1")
ex <- matrix(c(rchisq(100,1),rchisq(20,3),rchisq(20,6)),nrow=1)
rownames(ex) <- 'Gene-1'
plotGenePseudotime(sds, 'Gene-1', ex)

slingshot documentation built on Nov. 8, 2020, 5:51 p.m.