plotGeneCount {traviz} | R Documentation

## Plot gene expression in reduced dimension.

### Description

Plot the gene in reduced dimensional space.

### Usage

    plotGeneCount(curve, ...)

    ## S4 method for signature 'SlingshotDataSet'
    plotGeneCount(
      curve,
      counts = NULL,
      gene = NULL,
      clusters = NULL,
      models = NULL,
      title = NULL
    )

    ## S4 method for signature 'SingleCellExperiment'
    plotGeneCount(
      curve,
      counts = NULL,
      gene = NULL,
      clusters = NULL,
      models = NULL,
      title = NULL
    )

### Arguments

`curve` | One of two A `SlingshotDataSet` object. The output from trajectory inference using Slingshot. A `SingleCellExperiment` object. The output from trajectory inference using Slingshot.
`...` | parameters including:
`counts` | The count matrix, genes in rows and cells in columns. Only needed if the input is of the type `SlingshotDataSet` and the `gene` argument is not `NULL`.
`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 `clusters` argument.
`clusters` | The assignation of each cell to a cluster. Used to color the plot. Either `clusters` or `gene` and `counts` must be supplied.
`models` | The fitted GAMs, typically the output from `fitGAM`. Used to display the knots.
`title` | Title for the plot.

### Details

If both `gene` and `clusters` arguments are supplied, the plot will be colored according to gene count level. If none are provided, the function will fail.

### Value

A `ggplot` object

### Examples

    set.seed(97)
    library(slingshot)
    data(crv, package="traviz")
    data(counts, package="traviz")
    plotGeneCount(crv, counts, gene = "Mpo")

[Package traviz version 1.0.0 Index]