visIntegration: visIntegration
In CellMixS: Evaluate Cellspecific Mixing

Description Usage Arguments Details Value See Also Examples

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

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

`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.

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.

a ggplot object.

visCluster, ggridges

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)