plot_enrich2: Plotting function for hypergeometric enrichment

In BIGslu/BIGpicture: Standard Plots for BIGslu

Plotting function for hypergeometric enrichment

Description

Plotting function for hypergeometric enrichment

Usage

plot_enrich2(
  df = NULL,
  fdr_cutoff = 0.2,
  pathway_col = "pathway",
  gene_col = "genes",
  ratio_col = "k/K",
  fdr_col = "FDR",
  gssize_col = "n_pathway_genes",
  y_grouping_method = "fdr",
  include_gssize = FALSE,
  chart_style = "lollipop",
  fdr_binned_colors = c(0.001, 0.01, 0.05, 0.1, 0.2, 0.5, 0.99),
  fdr_continuous = FALSE,
  dot_sig_cutoff = NULL,
  dot_groupcol = "group"
)

Arguments

df	Data frame output by SEARchways::BIGprofiler or SEARchways::flexEnrich
fdr_cutoff	Numeric. Maximum FDR to plot. Default is 0.2.
pathway_col	Character string Column name for df column containing gene set names.
gene_col	Character string. Column name for df column containing gene lists names. Required if "y_grouping_method == 'hclust'".
ratio_col	Character string Column name for df column containing k/K ratios.
fdr_col	Character string. Column name for df column containing corrected p-values to plot.
gssize_col	Character string. Column name for df column containing gene set sizes.
y_grouping_method	Character string. Method for grouping gene sets along the y-axis. "hclust" (based on gene membership), "overlap_size", "gs_size", "ratio", "fdr", and "input". Default is "fdr".
include_gssize	Boolean. Whether or not to include a column of gene set sizes to the left of the enrichment plot. Default is FALSE.
chart_style	Character string. Options are "lollipop", "bar", and "dot". Default is "lollipop".
fdr_binned_colors	Numeric vector. Cutoffs for binned FDR value color groups for lollipop plots. Default is c(0.001, 0.01, 0.05, 0.1, 0.2, 0.5, 0.99).
fdr_continuous	Boolean. Whether or not to color points in a continuous fashions by a negative log transformed FDR value. Only applies to lollipop plots and dotplots.
dot_sig_cutoff	Numeric. What cutoff to use for applying a black outline to dotplot dots
dot_groupcol	Character string. Name of the column used to group enrichment along the x axis for dotplot.

Value

ggplot2 object

Examples

library(SEARchways)
library(dplyr)
#Run enrichment
gene_list <- list(HRV1 = names(example.gene.list[[1]]),
                  HRV2 = names(example.gene.list[[2]]))
enrich <- flexEnrich(gene_list, ID="ENSEMBL", category="H")

#Plot
plot_enrich2(enrich, fdr_cutoff = 0.5)

BIGslu/BIGpicture documentation built on Feb. 3, 2025, 10:31 a.m.