bubbleplot_pwys: Make bubble plots for the significance, DE proportion, and...

In jdreyf/ezlimmaplot: Bioinformatics plots using limma and ggplot2, some from output of ezlimma

Make bubble plots for the significance, DE proportion, and counts of pathway analysis

Description

Make bubble plots like clusterProfiler showing the significance, proportion of genes with p-value below 0.05, and counts per comparison per pathway. These are called "bubble plots" instead of "dot plots" because they represent the counts as an additional dimension of numerical (i.e. non-factor) data.

Usage

bubbleplot_pwys(
  tab,
  prefix.v = NULL,
  name = NA,
  type.sig = c("p", "FDR"),
  cut.sig = 0.05,
  ntop = 20,
  pwys_nm_size = 100,
  width = 8,
  height = 8,
  caption = TRUE,
  mixed = c("include", "exclude", "only")
)

Arguments

tab	Table of output from ezlimma::roast_*.
prefix.v	A vector of prefixes that prefix .p, .FDR, or .logFC in colnames(tab). These will be the comparisons shown in the plot. If NULL these are inferred from colnames(tab) that end with .p.
name	Name of file to create. Set to NA to plot to screen instead of to file; otherwise, "_bubbleplots.pdf" is appended to the name.
type.sig	Either "p" or "FDR"; type of significance to show.
cut.sig	Numeric in [0, 1]. Pathways need to have significance of type type.sig < cut.sig in a comparison to be shown on the dot plot.
ntop	Integer; number of top pathways to show.
pwys_nm_size	The maximum number of characters for pathway names. Longer names will be truncated.
width	Manual option for determining the output file width in inches.
height	Manual option for determining the output file height in inches.
caption	Logical; should the caption explaining the x-axis be included?
mixed	Character string. Should mixed statistics be included, should they be the only statistics included, or should they be excluded?

Value

Invisibly, a list of ggplot objects.

jdreyf/ezlimmaplot documentation built on Feb. 8, 2025, 2:25 a.m.