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Plot Pathway Analysis Results as a Dot Plot

Source: R/plot_pathway_dotplot.R
plot_pathway_dotplot.Rd

Creates a dot plot to visualize pathway enrichment analysis results, supporting both ORA and FGSEA formats.

Usage

plot_pathway_dotplot(exp_data, score_name, top_n = 10, maxPval = 0.05)

Arguments

exp_data

A `SummarizedExperiment` object containing pathway analysis results stored in the `metadata()`.

score_name

A character string indicating the metadata field where pathway results are stored. Default is `"resultsORA"`.

top_n

Number of top pathways to display. Default is `10`.

maxPval

Maximum adjusted p-value for filtering pathways (if `usePval = TRUE`). Default is `0.05`.

Value

A `ggplot2` dot plot object showing pathway enrichment.

Details

The function supports two types of enrichment results:

  • ORA (Over-Representation Analysis): requires columns `PAdj`, `GeneRatio`, and `Pathway`

  • FGSEA: requires columns `padj`, `size`, and `pathway`

When `usePval = TRUE`, the plot will show -log10 adjusted p-values on the x-axis, colored by significance. When `usePval = FALSE`, the plot will rank and size pathways by gene ratio or enrichment size.