plotGenePseudotime: Plot Gene Expression by Pseudotime

Description Usage Arguments Value Examples

Description

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

Usage

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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

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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.