summarizeGO: A simplified way to visualize enrichment in GO clusters
In jokergoo/simplifyGO: Simplify Functional Enrichment Results

summarizeGO

R Documentation

A simplified way to visualize enrichment in GO clusters

Description

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.

jokergoo/simplifyGO documentation built on Sept. 18, 2024, 9:45 p.m.