visIntegration {CellMixS} | R Documentation

## 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)

[Package CellMixS version 1.4.2 Index]