visGroup {CellMixS} | R Documentation

## visGroup

### Description

Plot group label in a reduced dimensional plot.

### Usage

    visGroup(sce, group, dim_red = "TSNE")

### Arguments

`sce` | A `SingleCellExperiment` object.
`group` | Character. Name of group/batch variable. Needs to be one of `names(colData(sce))`.
`dim_red` | Character. Name of embeddings to use as subspace for plotting. Default is "TSNE".

### Details

Plots a reduced dimension plot colored by group parameter. The dimesion reduction embedding can be specified, but only tsne embeddings will automatically be computed by `runTSNE`. Embeddings from data integration methods (e.g. mnn.correct) can be used as long as they are specified in `reducedDimNames(sce)`.

### Value

a `ggplot` object.

### See Also

`visOverview`, `visMetric`

Other visualize functions: `visCluster()`

### Examples

    library(SingleCellExperiment)
    sim_list <- readRDS(system.file("extdata/sim50.rds", package = "CellMixS"))
    sce <- sim_list[[1]][, c(1:50, 300:350)]

    visGroup(sce, "batch")

[Package CellMixS version 1.4.2 Index]