visMetric: visMetric
In CellMixS: Evaluate Cellspecific Mixing

Description Usage Arguments Details Value See Also Examples

Plot metric scores in a reduced dimensional plot.

1	visMetric(sce_cms, metric_var = "cms", dim_red = "TSNE", log10_val = FALSE)

`sce_cms`	A `SingleCellExperiment` object with the result scores (e.g. cms) to plot within `colData(res_object)`.
`metric_var`	Character Name of the metric scores to use. Default is "cms".
`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.

Plots a reduced dimension plot colored by metric scores. The dimension reduction embedding can be specified, but only tsne embeddings will automatically be computed using runTSNE. Embeddings from data integration methods (e.g. mnn.correct) can be used as long as they are present in reducedDimNames(sce).

a ggplot object.

visOverview, visGroup

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

library(SingleCellExperiment)
sim_list <- readRDS(system.file("extdata/sim50.rds", package = "CellMixS"))
sce <- sim_list[[1]][, c(1:30, 300:320)]
sce_cms <- cms(sce, "batch", k = 20, n_dim = 2)

visMetric(sce_cms)