R: visOverview

visOverview {CellMixS}

R Documentation

visOverview

Description

Plot an overview of metric results, group label and any colData variable in a reduced dimensional representation.

Usage

visOverview(sce_cms, group, metric_prefix = "cms", dim_red = "TSNE",
  log10_val = FALSE, other_var = NULL)

Arguments

`sce_cms`	A `SingleCellExperiment` object with the result scores (e.g. cms) to plot in `colData(sce_cms)`.
`group`	Character. Name of group/batch variable. Needs to be one of `names(colData(sce))`.
`metric_prefix`	Character. Prefix to specify names of `colData(sce)` to be plotted. 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.
`other_var`	Character string. Name(s) of other variables to be plotted asided. Need correspond to one of `colData(sce)`.

Details

Plots reduced dimensions of cells colored by group variable and metric score. If 'red_dim' is not defined in reducedDimNames(sce) a tsne is calculated using runTSNE. Other color label as celltype label or smoothened scores can be plotted aside. Embeddings from data integration methods (e.g. mnn.correct) can be used if they are specified in reducedDimNames(sce).

Value

a ggplot object.

Examples

library(SingleCellExperiment)
sim_list <- readRDS(system.file("extdata/sim50.rds", package = "CellMixS"))
sce <- sim_list[[1]][, c(1:30, 300:330)]
sce_cms <- cms(sce, "batch", k = 20, n_dim = 2)

visOverview(sce_cms, "batch", other_var = "batch")

[Package CellMixS version 1.0.2 Index]