visOverview {CellMixS} | R Documentation |
Plot an overview of metric results, group label and any colData variable in a reduced dimensional representation.
visOverview(sce_cms, group, metric_prefix = "cms", dim_red = "TSNE", log10_val = FALSE, other_var = NULL)
sce_cms |
A |
group |
Character. Name of group/batch variable. Needs to be one of
|
metric_prefix |
Character. Prefix to specify names of
|
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 |
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.
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")