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")
    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)

[Package slingshot version 1.6.1 Index]