Re-exported functions from other packages — RunEnrichment • biopipen.utils

enrichit::EnrichIt() (exported as RunEnrichment) - Enrichment analysis
enrichit::ParseGMT() - Parse GMT file

Usage

RunEnrichment(
  userlist,
  dbs,
  method = ifelse(tolower(style[1]) == "enrichr", "fisher", "hypergeometric"),
  use_matched_only = ifelse(tolower(style[1]) == "enrichr", FALSE, TRUE),
  padjust_method = c("BH", "bonferroni", "holm", "hochberg", "hommel", "BY", "fdr"),
  background = NULL,
  style = c("enrichr", "Enrichr", "clusterProfiler", "ClusterProfiler",
    "clusterprofiler"),
  return_all = FALSE
)

ParseGMT(gmtfile, swap_name_desc_if_needed = TRUE)

VizEnrichment(
  data,
  top_term = NULL,
  plot_type = c("bar", "dot", "lollipop", "network", "enrichmap", "wordcloud",
    "comparison", "heatmap"),
  x_by = NULL,
  size_by = NULL,
  fill_cutoff_name = NULL,
  fill_name = NULL,
  values_fill = 0,
  character_width = 50,
  expand = NULL,
  word_type = c("term", "feature"),
  split_by = NULL,
  split_by_sep = "_",
  facet_by = NULL,
  facet_scales = NULL,
  group_by = NULL,
  group_by_sep = "_",
  metric = "p.adjust",
  cutoff = NULL,
  palette = "Spectral",
  xlab = NULL,
  ylab = NULL,
  ...
)

Arguments

userlist

Vector of user-provided genes

dbs

List of gene sets or paths to GMT files It can be a vector of database names. You can set the names of the vector, which will be used as the database names. Otherwise a list is expected, where each element is a database (e.g. parsed from a gmt file). If a database is given directly (without a name), the expression of this argument will be used as the database name.

method

Method for computing p-value, either "fisher" or "hypergeometric" When style is "enrichr", the method defaults to "fisher". When style is "clusterProfiler", the method defaults to "hypergeometric".

use_matched_only

Logical, whether to use only matched genes against the gene sets. This will affect the number of genes in the user list when computing the p-value. By default, when style is "enrichr", this is set to FALSE. When style is "clusterProfiler", this is set to TRUE.

padjust_method

Method for adjusting p-values, either "BH", "bonferroni", "holm", "hochberg", "hommel", "BY", "fdr"

background

Vector of all genes in the universe or a number of genes in the universe. If NULL, the number of genes in the gene set will be used. For "enrichr", the default is 20,000. For "clusterProfiler", the default is the number of unique genes in the gene set. Note that for "enrichr", if a vector is given, the length of it will be used, no checking will be done to see if userlist and genes from dbs are in the vector.

style

Style of the output, either "enrichr" or "clusterProfiler"

return_all

Logical, whether to return all results (all gene sets in dbs) or only those with at least one gene in the user list.

gmtfile

Path to the GMT file

swap_name_desc_if_needed

Logical, whether to swap name and description fields. They will be swapped only if:

swap_name_desc_if_needed is TRUE; and
The descriptions are not empty; and
The descriptions are shorter than the names; and
The descriptions are not ID-like (i.e., hsa00001, or 123456).

data

A data frame with enrichment results. Must be the output of a clusterProfiler function (enrichGO, enrichKEGG, enrichPathway, enrichWP, etc.) or an enrichR result processed through plotthis::prepare_enrichr_result(). The function auto-detects the format based on column names.

top_term

Integer. Number of top terms (by significance) to display per group/facet combination. Default: 6 for all plot types except "enrichmap" which defaults to 100. Note that terms are not filtered globally — the top terms are selected independently within each combination of split_by, group_by, and facet_by levels.

plot_type

Character. The type of plot to generate. One of: "bar", "dot", "lollipop", "network", "enrichmap", "wordcloud", "comparison", or "heatmap". See the Description section for guidance on choosing a plot type. Default: "bar".

x_by

Character. Column name(s) to use for the x-axis. Works only for "dot" and "lollipop" plot types. Default: NULL (defaults to "GeneRatio" internally).

size_by

Character. Column name(s) to map to point size. Works only for "comparison", "dot", and "lollipop" plot types. Default: NULL (defaults to "GeneRatio" for comparison, "Count" for dot and lollipop).

fill_cutoff_name

Character. Legend label for terms that exceed the cutoff (shown in gray). Applies to "comparison", "dot", and "lollipop" plot types. Default: NULL (defaults to "Non-significant" when cutoff is set).

fill_name

Character. Legend title for the fill color scale (the significance metric). Applies to "comparison", "dot", and "lollipop" plot types. Default: NULL (auto-generated as "-log10(metric)").

values_fill

Numeric. The fill value for missing entries in the heatmap matrix. Used only for "heatmap" plot type. Default: 0.

character_width

Integer. Maximum character width for term descriptions before line-wrapping. Applies to all plot types; for "heatmap" the wrapping is deferred to the Heatmap function. Default: 50.

expand

Numeric vector of length 1, 2, or 4. Axis expansion factors passed to plotthis::BarPlot(). Used only for "bar" plot type. Default: NULL (defaults to c(0.1, 0.6, 0, 0.6)).

word_type

Character. What to display in the wordcloud. One of "term" (enrichment term descriptions) or "feature" (gene symbols from the enriched gene list). Used only for "wordcloud" plot type. Default: "term".

split_by

Character vector. Column name(s) in data to split the data and generate separate plots for each unique value. Multiple columns are concatenated with split_by_sep. Default: NULL.

split_by_sep

Character. Separator used when concatenating multiple split_by columns. Default: "_".

facet_by

Character vector. Column name(s) in data to use for faceting (generating sub-panels within each plot). Default: NULL.

facet_scales

Character. Facet scale behavior — "fixed" (same scales), "free", "free_x", or "free_y". Default: NULL (defaults to "free_y" for bar, dot, lollipop, and comparison plots).

group_by

Character vector. Column name(s) in data to group terms. Behavior depends on plot_type:

"comparison" — Groups are shown as x-axis categories in a dot plot comparing enrichment across groups. Required for this type.
"heatmap" — Groups are used as the columns of the heatmap (mapped to columns_by in plotthis::Heatmap()).
All other types — group_by is not supported and will raise an error. Use facet_by or split_by instead.

Multiple columns are concatenated with group_by_sep. Default: NULL.

group_by_sep

Character. Separator used when concatenating multiple group_by columns. Used only for "comparison" plot type. Default: "_".

metric

Character. The column name in data to use as the significance metric for ordering and coloring terms. Common choices are "p.adjust" (default), "pvalue", or "qvalue". When the metric is a p-value column, a \(-log_{10}\) transformation is applied automatically so that more significant terms have higher values.

cutoff

Numeric. A significance threshold to mark on the plot. Default: NULL (no marking). The behavior depends on plot_type:

"bar" — Adds a vertical dashed line at the transformed cutoff (e.g., \(-log_{10}(0.05)\)).
"dot", "lollipop", "comparison" — Terms above the cutoff are colored gray with the legend label from fill_cutoff_name.
"heatmap" — Adds asterisk (*) labels to cells where the metric exceeds the cutoff.
"network", "enrichmap", "wordcloud" — No effect.

This parameter only marks terms — it does not filter them. Use top_term to control how many terms are shown.

palette

Character. Color palette name for the fill scale. See plotthis::show_palettes() for available palettes. Default: "Spectral".

xlab

Character. Custom x-axis label. Default: NULL (auto-generated based on plot type and x_by/metric).

ylab

Character. Custom y-axis label. Default: NULL (auto-generated based on plot type).

...

Additional arguments passed to the underlying plotthis plotting function, determined by plot_type:

"bar": plotthis::BarPlot()
"dot": plotthis::DotPlot()
"lollipop": plotthis::LollipopPlot()
"network": plotthis::EnrichNetwork()
"enrichmap": plotthis::EnrichMap()
"wordcloud": plotthis::WordCloudPlot()
"comparison": plotthis::DotPlot()
"heatmap": plotthis::Heatmap()

Examples

if (FALSE) { # \dontrun{
  # See following links for examples
  # https://pwwang.github.io/enrichit/reference/EnrichIt.html
  # https://pwwang.github.io/enrichit/reference/ParseGMT.html
} # }