plot_clust_enrichments: Plot Cluster Enrichments

In dputhier/scigenex: The scigenex package (Single-Cell Informative GENe Explorer)

Plot Cluster Enrichments

Description

Plot Cluster Enrichments

Display cluster enrichments for gene GO terms.

Usage

plot_clust_enrichments(
  object,
  stat_shown = c("qvalue", "p.adjust", "pvalue"),
  nb_go_term = 3,
  gradient_palette = colors_for_gradient("Ju1"),
  label_fun = NULL,
  term_order = NULL,
  return_mat = FALSE,
  floor = NULL
)

Arguments

object	An object of class "ClusterSet".
stat_shown	A character string specifying the statistic to be shown. Must be one of "qvalue", "p.adjust", or "pvalue". Defaults to "qvalue".
nb_go_term	An integer specifying the number of top GO terms to select per cluster. Defaults to 6. Note that some terms may be shared between clusters.
gradient_palette	A vector of colors specifying the gradient palette for the color scale. Defaults to colors_for_gradient("Magma").
label_fun	A function to customize the labels of the GO terms. Defaults to NULL.
term_order	A vector specifying the desired order of the GO terms. Defaults to NULL.
return_mat	Logical. Do not return a ggplot object but the prepared matrix.
floor	A value for flooring the statistic.

Value

A ggplot object displaying the cluster enrichments for the GO terms.

See Also

enrich_go colors_for_gradient

Examples

load_example_dataset("8028226/files/pbmc3k_medium_clusters_enr_sub")
plot_clust_enrichments(pbmc3k_medium_clusters_enr_sub)

dputhier/scigenex documentation built on Dec. 20, 2024, 2:22 a.m.