visOverview: visOverview

In almutlue/CellMixS: Evaluate Cellspecific Mixing

visOverview

Description

Plot an overview of metric results, group label and any colData variable in a reduced dimensional representation.

Usage

visOverview(
  sce_cms,
  group,
  metric = "cms",
  prefix = TRUE,
  dim_red = "TSNE",
  log10_val = FALSE,
  other_var = NULL,
  metric_prefix = NULL
)

Arguments

sce_cms	A SingleCellExperiment object with the result scores (e.g. cms) to plot in colData(sce_cms).
group	Character. Name of group/batch variable. Needs to be one of names(colData(sce)).
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).
dim_red	Character. Name of embeddings to use as subspace for plotting. Default is "TSNE".
log10_val	Logical. Indicating if -log10(metric) should be plotted.
other_var	Character string. Name(s) of other variables to be plotted asided. Need correspond to one of colData(sce).
metric_prefix	Former parameter to define prefix of the metric to be plotted. Will stop and ask for the new syntax.

Details

Plots reduced dimensions of cells colored by group variable and metric score. If 'red_dim' is not defined in reducedDimNames(sce) a tsne is calculated using runTSNE. Other color label as celltype label or smoothened scores can be plotted aside. Embeddings from data integration methods (e.g. mnn.correct) can be used if they are specified in reducedDimNames(sce).

Value

a ggplot object.

See Also

visMetric, visGroup

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

Examples

library(SingleCellExperiment)
sim_list <- readRDS(system.file("extdata/sim50.rds", package = "CellMixS"))
sce <- sim_list[[1]][, c(1:30, 300:330)]
sce_cms <- cms(sce, "batch", k = 20, n_dim = 2)

visOverview(sce_cms, "batch", other_var = "batch")

almutlue/CellMixS documentation built on March 14, 2023, 8:23 a.m.