simplifyGO: Simplify Gene Ontology (GO) enrichment results

In jokergoo/simplifyEnrichment: Simplify Functional Enrichment Results

Simplify Gene Ontology (GO) enrichment results

Description

Simplify Gene Ontology (GO) enrichment results

Usage

simplifyGO(
  mat,
  method = "binary_cut",
  control = list(),
  plot = TRUE,
  verbose = TRUE,
  column_title = qq("@{nrow(mat)} GO terms clustered by '@{method}'"),
  ht_list = NULL,
  ...
)

simplifyEnrichment(...)

Arguments

mat	A GO similarity matrix. You can also provide a vector of GO IDs to this argument.
method	Method for clustering the matrix. See cluster_terms().
control	A list of parameters for controlling the clustering method, passed to cluster_terms().
plot	Whether to make the heatmap.
verbose	Whether to print messages.
column_title	Column title for the heatmap.
ht_list	A list of additional heatmaps added to the left of the similarity heatmap.
...	Arguments passed to ht_clusters().

Details

This is basically a wrapper function that it first runs cluster_terms() to cluster GO terms and then runs ht_clusters() to visualize the clustering.

The arguments in simplifyGO() passed to ht_clusters() are:

• draw_word_cloud: Whether to draw the word clouds.

• min_term: Minimal number of GO terms in a cluster. All the clusters with size less than min_term are all merged into one single cluster in the heatmap.

• order_by_size: Whether to reorder GO clusters by their sizes. The cluster that is merged from small clusters (size < min_term) is always put to the bottom of the heatmap.

• stat: What values of keywords are used to map to font sizes in the word clouds.

• exclude_words: Words that are excluded in the word cloud.

• max_words: Maximal number of words visualized in the word cloud.

• word_cloud_grob_param: A list of graphic parameters passed to word_cloud_grob().

• fontsize_range The range of the font size. The value should be a numeric vector with length two. The minimal font size is mapped to word frequency value of 1 and the maximal font size is mapped to the maximal word frequency. The font size interlopation is linear.

• bg_gp: Graphic parameters for controlling the background of word cloud annotations.

Value

A data frame with two columns: GO IDs and cluster labels.

Examples

set.seed(123)
go_id = random_GO(500)
mat = GO_similarity(go_id)
df = simplifyGO(mat, word_cloud_grob_param = list(max_width = 80))
head(df)

jokergoo/simplifyEnrichment documentation built on Sept. 16, 2024, 8:39 a.m.