visIntegration {CellMixS}R Documentation

visIntegration

Description

Creates a summary plot of metric scores (for different integration methods).

Usage

visIntegration(res_object, metric_prefix = "cms", violin = FALSE)

Arguments

res_object

SingleCellExperiment object, list, matrix or data.frame. The SingleCellExperiment object should contain the result scores (cms) to compare within colData(res_object). List, matrix or data frame should have result scores in list elements resp. columns.

metric_prefix

Character. Prefix to specify names of colData(sce) to be compared. Applys only if 'res_object' is a SingleCellExperiment object. Default is 'cms'.

violin

A logical. If true violin plots are plotted, while the default (FALSE) will plot ridge plots.

Details

Plots summarized cms scores from an SingleCellExperiment object, list or dataframe. This function is intended to visualize and compare different methods and views of the same dataset, not to compare different datasets.

Value

a ggplot object.

See Also

visCluster, ggridges

Examples

library(SingleCellExperiment)

sim_list <- readRDS(system.file("extdata/sim50.rds", package = "CellMixS"))

sce <- sim_list[["batch20"]][, c(1:30,300:320)]
sce_mnn <- cms(sce,"batch", k = 20, dim_red = "MNN", res_name = "MNN",
n_dim = 2)

visIntegration(sce_mnn, metric_prefix = "cms.", violin = TRUE)


[Package CellMixS version 1.0.0 Index]