visHist: visHist

In CellMixS: Evaluate Cellspecific Mixing

Description

Plot pvalue histograms of metric score distributions

Usage

visHist(
  res_object,
  metric = "cms",
  prefix = TRUE,
  n_col = 1,
  metric_prefix = NULL
)

Arguments

res_object	SingleCellExperiment object, matrix or data.frame. The SingleCellExperiment object should contain the result scores (e.g. cms) to plot in colData(res_object). Matrix or data frame should have result scores in columns and cells in rows.
metric	Character vector. Specify names of colData(sce) to be plotted. Applys only if 'res_object' is a SingleCellExperiment object. Default is 'cms'. If prefix is TRUE all columns starting with 'metric' will be plotted.
prefix	Boolean. Is ‘metric' used to specify column’s prefix(true) or complete column names (False).
n_col	Numeric. Number of columns of the pval histogram.
metric_prefix	Former parameter to define prefix of the metric to be plotted. Will stop and ask for the new syntax.

Details

Plots metric score distribution similar to a pvalue histogram distribution. Without dataset-specific bias, cms scores should be approx. flat distributed. If 'res_object' is a matrix or data.frame, it will create a histogram for each column. If 'res_object' is a SingleCellExperiment object, it will create a histogram of all colData(res_object) that start with or are specified in 'metric'.

Value

a ggplot object.

See Also

Other visualize metric functions: visMetric(), visOverview()

Examples

library(SingleCellExperiment)
sim_list <- readRDS(system.file("extdata/sim50.rds", package = "CellMixS"))
sce <- sim_list[[1]][, c(1:50)]
sce_cms <- cms(sce, "batch", k = 20, n_dim = 2)
visHist(sce_cms)

CellMixS documentation built on Dec. 19, 2020, 2 a.m.