visIntegration | R Documentation |
Creates a summary plot of metric scores (for different integration methods).
visIntegration( res_object, metric = "cms", prefix = TRUE, violin = FALSE, metric_name = "metric", metric_prefix = NULL )
res_object |
|
metric |
Character vector. Specify names of |
prefix |
Boolean. Is ‘metric' used to specify column’s prefix(true) or complete column names (False). |
violin |
A logical. If true violin plots are plotted, while the default (FALSE) will plot ridge plots. |
metric_name |
Character. Name of the score metric. |
metric_prefix |
Former parameter to define prefix of the metric to be plotted. Will stop and ask for the new syntax. |
Plots summarized cms scores from an SingleCellExperiment
object, list or dataframe. This function is intended to visualize and
compare different methods and views of the same dataset, not to compare
different datasets.
a ggplot
object.
visCluster
, ggridges
library(SingleCellExperiment) sim_list <- readRDS(system.file("extdata/sim50.rds", package = "CellMixS")) sce <- sim_list[["batch20"]][, c(1:30,300:320)] sce_mnn <- cms(sce,"batch", k = 20, dim_red = "MNN", res_name = "MNN", n_dim = 2) visIntegration(sce_mnn, metric = "cms.", violin = TRUE)
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