visIntegration: visIntegration

In almutlue/CellMixS: Evaluate Cellspecific Mixing

visIntegration

Description

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

Usage

visIntegration(
  res_object,
  metric = "cms",
  prefix = TRUE,
  violin = FALSE,
  metric_name = "metric",
  metric_prefix = NULL
)

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	Character vector. Specify names of colData(sce) to be compared. Applys only if 'res_object' is a SingleCellExperiment object. Default is 'cms'. If prefix is TRUE all columns starting with 'metric' will be compared and plotted.
prefix	Boolean. Is ‘metric' used to specify column’s prefix(true) or complete column names (False).
violin	A logical. If true violin plots are plotted, while the default (FALSE) will plot ridge plots.
metric_name	Character. Name of the score metric.
metric_prefix	Former parameter to define prefix of the metric to be plotted. Will stop and ask for the new syntax.

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 = "cms.", violin = TRUE)

almutlue/CellMixS documentation built on Sept. 8, 2024, 12:45 p.m.