geom_gsea: create a venn diagram in ggplot2

View source: R/geom_gsea.R

geom_gseaR Documentation

create a venn diagram in ggplot2

Description

Imports: ggplot2

Usage

geom_gsea(
  df,
  labelsize = 4,
  zeroline = F,
  prettyGSEA = T,
  ncol = NULL,
  nrow = NULL,
  linecolor = "green",
  linesize = 1,
  tickcolor = "black",
  ticksize = 0.5,
  zerocolor = "black",
  zerosize = 0.5,
  zerotype = "dashed",
  ...
)

Arguments

df

data.frame, calculated by the function gseaCurve

labelsize

number, font size of the statistics (if gsea is provided)

zeroline

boolean, should a zero line be displayed?

prettyGSEA

boolean, should some aesthetics be automatically added? Adds a 0-line, regulates y-breaks and labels the axes.

ncol

Number of rows and columns.

nrow

Number of rows and columns.

linecolor

string, color of the main gsea line

linesize

number, thickness of the main gsea line

tickcolor

string, color of the ticks representing hit genes

ticksize

number, thickness of the ticks representing hit genes

zerocolor

string, color of the zeroline

zerosize

number, thickness of the zeroline

zerotype

string, linetype of the zeroline (e.g. "dotted")

...

Other arguments passed on to layer(). These are often aesthetics, used to set an aesthetic to a fixed value, like colour = "red" or size = 3. They may also be parameters to the paired geom/stat.

Details

uses the functions geom_gseaLine, geom_gseaTicks and geom_gseaGradient, from this package

Value

a list of ggplot layers, ready to be added to a ggplot object

Examples

library(gggsea)
library(ggplot)

curve <- gseaCurve(myRankedlist, mySetlist)
ggplot() + geom_gsea(curve) + theme_gsea()


NicolasH2/gggsea documentation built on Jan. 28, 2024, 7:25 p.m.