Plot Cluster Enrichments

Plot Cluster Enrichments

Display cluster enrichments for gene GO terms.

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")
#> |-- INFO :  Dataset 8028226/files/pbmc3k_medium_clusters_enr_sub was already loaded. 
plot_clust_enrichments(pbmc3k_medium_clusters_enr_sub)