rliger (version 2.2.0)

plotGODot: Visualize GO enrichment test result in dot plot

Description

Visualize GO enrichment test result in dot plot

Usage

plotGODot(
  result,
  group = NULL,
  query = NULL,
  pvalThresh = 0.05,
  n = 20,
  minDotSize = 3,
  maxDotSize = 7,
  termIDMatch = "^GO",
  colorPalette = "E",
  colorDirection = -1,
  ...
)

Value

A ggplot object.

Arguments

result

Returned list object from runGOEnrich.

group

A single group name to be visualized, must be available in names(result). Default NULL make plots for the first group.

query

A single string selecting from which query to show the result. Choose from "Up" for results using up-regulated genes, "Down" for down-regulated genes. Default NULL use the first available.

pvalThresh

Numeric scalar, cutoff for p-value where smaller values are considered as significant. Default 0.05.

n

Number of top terms to be shown, ranked by p-value. Default 20.

minDotSize

The size of the dot representing the minimum gene count. Default 3.

maxDotSize

The size of the dot representing the maximum gene count.

termIDMatch

Regular expression pattern to match the term ID. Default "^GO" for only using GO terms from returned results.

colorPalette, colorDirection

Viridis palette options. Default "E" and 1.

...

Arguments passed on to .ggplotLigerTheme

legendColorTitle

Legend title text for color aesthetics, often used for categorical or continuous coloring of dots. Default NULL shows the original variable name.

legendSizeTitle

Legend title text for size aesthetics, often used for sizing dots by continuous variable. Default NULL shows the original variable name.

showLegend

Whether to show the legend. Default TRUE.

legendPosition

Text indicating where to place the legend. Choose from "top", "bottom", "left" or "right". Default "right".

baseSize

One-parameter control of all text sizes. Individual text element sizes can be controlled by other size arguments. "Title" sizes are 2 points larger than "text" sizes when being controlled by this.

titleSize,xTitleSize,yTitleSize,legendTitleSize

Size of main title, axis titles and legend title. Default NULL controls by baseSize + 2.

subtitleSize,xTextSize,yTextSize,legendTextSize

Size of subtitle text, axis texts and legend text. Default NULL controls by baseSize.

plotly

Whether to use plotly to enable web based interactive browsing for the plot. Requires installation of package "plotly". Default FALSE.

Examples

# \donttest{
if (requireNamespace("gprofiler2", quietly = TRUE)) {
   go <- runGOEnrich(deg.pw)
   plotGODot(go)
}
# }