plot_pathways: Modern Gene Ontology / pathway-enrichment plots

In MosaiClusteR: An Umbrella Framework for Multi-Source and Multi-Omics Clustering

Modern Gene Ontology / pathway-enrichment plots

Description

Publication-quality replacements for the classic green GO DAG and the horizontal bar plot. Given the output of PathwayAnalysis() (or a single MLP result table) it draws either a dot plot that compares the enriched terms across clusters (the enrichment-map / clusterProfiler::dotplot idiom) or a lollipop plot for a single cluster. Dot area encodes the number of genes in the term and colour encodes -\log_{10} p on a perceptually-uniform viridis scale.

Usage

plot_pathways(
  pathways,
  style = c("dotplot", "lollipop", "circular"),
  top = 8,
  cluster = NULL,
  source = 1,
  title = NULL,
  palette = "D",
  max_chars = 42,
  wrap = 20,
  cluster_cols = NULL
)

Arguments

pathways	Output of PathwayAnalysis() (a list of sources, each a list of per-cluster results carrying a ⁠$Pathways⁠ table), a single source's per-cluster list, or a single MLP/data.frame result table.
style	"dotplot" to compare clusters side by side, "lollipop" for one cluster, or "circular" for a radial (sunburst-style) bar plot that groups the terms by cluster around a central hub; bar length encodes -\log_{10} p, colour encodes the cluster, and each term is a single-line radial label that stays legible as the number of terms grows.
top	Number of top terms (by p-value) to show per cluster.
cluster	For "lollipop" (or to subset a dot plot): which cluster to show, by name (e.g. "Cluster 1") or index. NULL shows all.
source	Which source (index or name) of a full PathwayAnalysis() object to plot. Default 1.
title	Optional plot title.
palette	viridis option passed to ggplot2::scale_colour_viridis_c() ("D" viridis, "C" plasma, "B" inferno, "G" mako, ...).
max_chars	Term descriptions longer than this are wrapped onto two lines for legibility (dot plot / lollipop).
wrap	For style = "circular", the character width at which long term labels are wrapped onto successive lines, so long names stay compact and legible around the ring. Smaller values wrap more aggressively.
cluster_cols	For style = "circular", an optional vector of fill colours for the clusters (cluster bars and legend). Supply the same palette used elsewhere - e.g. the cols passed to Cyclogram() - so the clusters share one colour scheme across figures. Positional by cluster order, or a vector named by cluster. Default NULL uses the package palette.

Value

A ggplot object (invisibly); it is also printed so the function works directly on an open graphics device.

See Also

PathwayAnalysis(), PlotPathways()

Examples

## Not run: 
P <- PathwayAnalysis(List = L, geneExpr = ge, nrclusters = 3,
                     method = c("limma", "MLP"), geneInfo = geneInfo,
                     geneSetSource = "GOBP", sign = 0.05, niter = 2)
plot_pathways(P, style = "dotplot", top = 8)          # compare clusters
plot_pathways(P, style = "lollipop", cluster = 1)     # one cluster

## End(Not run)

MosaiClusteR documentation built on Oct. 25, 2026, 1:08 a.m.