plot_volcano: Plots a volcano plot with ggplot2

View source: R/plot_volcano.R

plot_volcanoR Documentation

Plots a volcano plot with ggplot2

Description

Plots a volcano plot with ggplot2

Usage

plot_volcano(
  data_,
  color = "regulated",
  p.value.cutoff = 0.05,
  pos.log2fc.cutoff = 0,
  neg.log2fc.cutoff = 0,
  highlight.variables = NULL,
  highlight.color = NULL,
  x.axis.title = "log2 fold-change",
  y.axis.title = "-log10(p-value)",
  text.size = 6,
  text.color = "black",
  point.size = 2,
  point.alpha = 0.8,
  highlight.point.size = 3,
  highlight.point.alpha = 0.8,
  x.axis.breaks = 1,
  y.axis.breaks = 1,
  axis.line.size = 0.5,
  axis.color = "black",
  axis.ticks.size = 0.3,
  axis.title.size = 8,
  axis.text.size = 6,
  aspect.ratio = 0.8,
  use.plotly,
  view = T,
  input = "data_t.test",
  output = "plot_t.test"
)

Arguments

data_

data_

color

column for color of points

p.value.cutoff

p-value limit for coloring

pos.log2fc.cutoff

positive log2 fold-change limit for coloring

neg.log2fc.cutoff

negative log2 fold-change limit for coloring

highlight.variables

variables to highlight by point.size

highlight.color

color to use to highlight proteins

x.axis.title

title of x-axis

y.axis.title

title of y-axis

text.size

size of text in points (5-8)

text.color

color of text

point.size

point size (0.5-2)

point.alpha

transparency (0-1)

highlight.point.size

size of point of highlighted variables

highlight.point.alpha

transparency of points to be highlighted

x.axis.breaks

break size between ticks of x-axis

y.axis.breaks

break size between ticks of y-axis

axis.line.size

width of axes lines

axis.color

color of axes lines

axis.ticks.size

width of axis ticks

axis.title.size

size of axis title

axis.text.size

size of axis labels

aspect.ratio

y/x ratio

use.plotly

make interactive plots with ggplotly() (default: T if html document)

view

view plot

input

name of input data

output

name of output data


nicohuttmann/pOmics documentation built on Sept. 21, 2022, 9:28 a.m.