visCluster: visCluster

In almutlue/CellMixS: Evaluate Cellspecific Mixing

visCluster

Description

Creates summary plots of metric scores for different groups/cluster.

Usage

visCluster(sce_cms, cluster_var, metric_var = "cms", violin = FALSE)

Arguments

sce_cms	A SingleCellExperiment object with the result scores (e.g. cms) to plot within colData(res_object).
cluster_var	Character. Name of the factor level variable to summarize metric scores on.
metric_var	Character Name of the metric scores to use. Default is "cms".
violin	A logical. If true violin plots are plotted, while the default (FALSE) will plot ridge plots.

Details

Plots summarized metric scores. This function is intended to visualize and compare metric scores among clusters or other dataset variables spcified in 'cluster_var'.

Value

a ggplot object.

See Also

visIntegration

Other visualize functions: visGroup()

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)

visCluster(sce_cms, "batch")

almutlue/CellMixS documentation built on March 14, 2023, 8:23 a.m.