visOverview: visOverview

Description Usage Arguments Details Value See Also Examples

View source: R/VisCms.R

Description

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

Usage

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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

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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 Dec. 22, 2020, 11:07 a.m.