R: Plot Gene Expression by Pseudotime

plotGenePseudotime {slingshot}

R Documentation

Plot Gene Expression by Pseudotime

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")
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)

[Package slingshot version 1.0.0 Index]