summarizeGO: A simplified way to visualize enrichment in GO clusters

In jokergoo/simplifyGO: Simplify Functional Enrichment Results

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.

1. specify value as a named vector where GO IDs are the names. 2. specify value as a list of numeric named vectors. In this case, value contains multiple enrichment results.

Examples

# There is no example
NULL

jokergoo/simplifyGO documentation built on Oct. 25, 2023, 9:02 p.m.