dotplot_pwys: Make dot plots for the significance and DE proportion of...

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

Make dot plots for the significance and DE proportion of pathway analysis

Description

Make dot plots like clusterProfiler showing the significance and proportion of genes in each pathway with significance below cutoff.

Usage

dotplot_pwys(
  tab,
  prefix.v = NULL,
  name = NA,
  type.sig = c("p", "FDR"),
  cut.sig = 0.05,
  ntop = 20,
  pwys_nm_size = 100,
  font.size = 12,
  width = 8,
  height = 8,
  mixed = c("include", "exclude", "only"),
  reorder.rows = TRUE,
  caption = TRUE,
  colorbar.title = "Prop P<5%"
)

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, "_dotplot.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 pathway-by-comparison statistics to select.
pwys_nm_size	The maximum number of characters for pathway names. Longer names will be truncated.
font.size	Numeric font size of pathway names e.g. 12.
width	Manual option for determining the output file width in inches.
height	Manual option for determining the output file height in inches.
mixed	Character string. Should mixed statistics be included, should they be the only statistics included, or should they be excluded?
reorder.rows	Boolean; reorder pathways by significance before selecting ntop pathways? If not, order of tab is retained.
caption	Logical; should the caption explaining the color bar title be included?
colorbar.title	Character title of color bar.

Value

Invisibly, the ggplot object.

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