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Enrichment Map

Source: R/enrich.R
EnrichMap.Rd

Creates enrichment map visualizations showing clustering of enriched terms based on gene overlap. Terms are nodes, and edges represent shared genes. Nodes are clustered to reveal functional modules.

Usage

EnrichMap(
  data,
  in_form = c("auto", "clusterProfiler", "clusterprofiler", "enrichr"),
  split_by = NULL,
  split_by_sep = "_",
  top_term = 10,
  metric = "p.adjust",
  layout = "fr",
  minchar = 2,
  cluster = "fast_greedy",
  show_keyword = FALSE,
  nlabel = 4,
  character_width = 50,
  mark = "ellipse",
  label = c("term", "feature"),
  labelsize = 5,
  expand = c(0.4, 0.4),
  words_excluded = NULL,
  theme = "theme_ggforge",
  theme_args = list(),
  palette = "Paired",
  palcolor = NULL,
  alpha = 1,
  aspect.ratio = NULL,
  legend.position = "right",
  legend.direction = "vertical",
  title = NULL,
  subtitle = NULL,
  xlab = NULL,
  ylab = NULL,
  seed = 8525,
  combine = TRUE,
  nrow = NULL,
  ncol = NULL,
  byrow = TRUE,
  axes = NULL,
  axis_titles = axes,
  guides = NULL,
  design = NULL,
  ...
)

Arguments

data

A data frame containing the data to be plotted. It should be in the format of clusterProfiler enrichment result, which includes the columns: ID, Description, GeneRatio, BgRatio, pvalue, p.adjust, qvalue, geneID and Count.

  • The ID, qvalue and Count columns are optional.

  • The Description is the description of the term.

  • The GeneRatio is the number of genes in the term divided by the total number of genes in the input list.

  • The BgRatio is the number of genes in the term divided by the total number of genes in the background list (all terms).

  • The Count column, if given, should be the same as the first number in GeneRatio.

If you have enrichment results from multiple databases, you can combine them into one data frame and add a column (e.g. Database) to indicate the database. You can plot them in a single plot using the split_by argument (e.g. split_by = "Database").

in_form

A character string specifying the input format. Either "auto", "clusterProfiler", "clusterprofiler" or "enrichr". The default is "auto", which will try to infer the input format.

split_by

Column name(s) to split data into multiple plots

split_by_sep

Separator when concatenating multiple split_by columns

top_term

An integer specifying the number of top terms to show.

metric

A character string specifying the metric to use for the size of the nodes. It is also used to order the terms when selected the top terms. Either "pvalue" or "p.adjust". The default is "p.adjust".

layout

A character string specifying the layout of the graph. Either "circle", "tree", "grid" or other layout functions in igraph.

minchar

An integer specifying the minimum number of characters to show in the keyword.

cluster

A character string specifying the clustering method. Either "fast_greedy", "walktrap", "edge_betweenness", "infomap" or other clustering functions in igraph.

show_keyword

A logical value specifying whether to show the keyword instead of Description/Term in the plot.

nlabel

An integer specifying the number of labels to show in each cluster.

character_width

The width of the characters used to wrap the keyword.

mark

A character string specifying the mark to use for the nodes. Either "ellipse", "rect", "circle", "text" or other mark functions in ggforce.

label

A character string specifying the label to show in the legend. Either "term" or "feature". The default is "term".

labelsize

A numeric value specifying the size of the label.

expand

Expansion values for plot axes (CSS-like padding)

words_excluded

A character vector specifying the words to exclude in the keyword.

theme

Theme name (string) or theme function

theme_args

List of arguments passed to theme function

palette

Color palette name

palcolor

Custom colors for palette

alpha

Transparency level (0-1)

aspect.ratio

Aspect ratio of plot panel

legend.position

Legend position: "none", "left", "right", "bottom", "top"

legend.direction

Legend direction: "horizontal" or "vertical"

title

Plot title

subtitle

Plot subtitle

xlab

X-axis label

ylab

Y-axis label

seed

Random seed for reproducibility

combine

Whether to combine split plots into one

nrow

Number of rows when combining plots

ncol

Number of columns when combining plots

byrow

Fill combined plots by row

axes

How to handle axes in combined plots ("keep", "collect", "collect_x", "collect_y")

axis_titles

How to handle axis titles in combined plots

guides

How to handle guides in combined plots ("collect", "keep", "auto")

design

Custom layout design for combined plots

...

Additional arguments passed to atomic plotting functions.

Value

A ggplot object or wrap_plots object or a list of ggplot objects

Examples

# \donttest{
data(enrich_example)
EnrichMap(enrich_example)

EnrichMap(enrich_example, label = "feature")

EnrichMap(enrich_example, show_keyword = TRUE, label = "term")

EnrichMap(enrich_example, show_keyword = TRUE, label = "feature")


data(enrich_multidb_example)
EnrichMap(enrich_multidb_example, split_by = "Database")

EnrichMap(enrich_multidb_example,
  split_by = "Database",
  palette = list(DB1 = "Paired", DB2 = "Set1")
)

# }