A simplified way to visualize enrichment in GO clusters

Usage

summarizeGO(
  go_id,
  value = NULL,
  aggregate = mean,
  method = "binary_cut",
  control = list(),
  verbose = TRUE,
  axis_label = "Value",
  title = "",
  legend_title = axis_label,
  min_term = round(nrow(mat) * 0.01),
  stat = "pvalue",
  min_stat = ifelse(stat == "count", 5, 0.05),
  exclude_words = character(0),
  max_words = 6,
  word_cloud_grob_param = list(),
  fontsize_range = c(4, 16),
  bg_gp = gpar(fill = "#DDDDDD", col = "#AAAAAA")
)

Arguments

go_id: A vector of GO IDs.
value: A list of numeric value associate with go_id. We suggest to use -log10(p.adjust) or -log2(fold enrichment) as the values.
aggregate: Function to aggregate values in each GO cluster.
method: Method for clustering the matrix. See cluster_terms().
control: A list of parameters for controlling the clustering method, passed to cluster_terms().
verbose: Whether to print messages.
axis_label: X-axis label.
title: Title for the whole plot.
legend_title: Title for the legend.
min_term: Minimal number of functional terms in a cluster. All the clusters with size less than min_term are all merged into one separated cluster in the heatmap.
stat: Type of value for mapping to the font size of keywords in the word clouds. There are two options: "count": simply number of keywords; "pvalue": enrichment on keywords is performed (by fisher's exact test) and -log10(pvalue) is used to map to font sizes.
min_stat: Minimal value for stat for selecting keywords.
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 font size interpolation is linear.
bg_gp: Graphics parameters for controlling word cloud annotation background.

Details

There are several other ways to specify GO IDs and the associated values.

specify value as a named vector where GO IDs are the names.
specify value as a list of numeric named vectors. In this case, value contains multiple enrichment results.

Please refer to https://jokergoo.github.io/2023/10/02/simplified-simplifyenrichment-plot/ for more examples of this function.