visOverview: visOverview
In CellMixS: Evaluate Cellspecific Mixing

Description Usage Arguments Details Value See Also Examples

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

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

`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.

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).

a ggplot object.

visMetric, visGroup

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

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")