visMetric {CellMixS} | R Documentation

## visMetric

### Description

Plot metric scores in a reduced dimensional plot.

### Usage

    visMetric(sce_cms, metric_var = "cms", dim_red = "TSNE", log10_val = FALSE)

### Arguments

`sce_cms` | A `SingleCellExperiment` object with the result scores (e.g. cms) to plot within `colData(res_object)`.
`metric_var` | Character Name of the metric scores to use. Default is "cms".
`dim_red` | Character. Name of embeddings to use as subspace for plotting. Default is "TSNE".
`log10_val` | Logical. Indicating if -log10(metric) should be plotted.

### Details

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

### Value

a `ggplot` object.

### See Also

`visOverview`, `visGroup`

Other visualize metric functions: `visHist()`, `visOverview()`

### Examples

    library(SingleCellExperiment)
    sim_list <- readRDS(system.file("extdata/sim50.rds", package = "CellMixS"))
    sce <- sim_list[[1]][, c(1:30, 300:320)]
    sce_cms <- cms(sce, "batch", k = 20, n_dim = 2)

    visMetric(sce_cms)

[Package CellMixS version 1.4.2 Index]