VolcanoView: Volcano View

In WubingZhang/MAGeCKFlute: Integrative Analysis Pipeline for Pooled CRISPR Functional Genetic Screens

Volcano View

Description

Volcano plot for differential analysis.

Usage

VolcanoView(
  df,
  x = "logFC",
  y = "adj.P.Val",
  Label = NA,
  top = 5,
  topnames = NULL,
  x_cutoff = log2(1.5),
  y_cutoff = 0.05,
  mycolour = c("gray80", "#e41a1c", "#377eb8"),
  alpha = 0.6,
  force = 0.1,
  main = NULL,
  xlab = "log2FC",
  ylab = "-log10(FDR)",
  filename = NULL,
  width = 4,
  height = 2.5,
  ...
)

Arguments

df	A data frame.
x	A character, specifying the x-axis in Volcanno figure, 'logFC' (default).
y	A character, specifying the y-axis in Volcanno figure, 'adj.P.Val' (default). log10 transformation will be done automatically.
Label	A character, specifying dots to be labeled on the figure.
top	An integer, specifying the number of top significant genes to be labeled.
topnames	A character vector, indicating positive/negative controls to be labeled.
x_cutoff	Numeric, specifying cutoff of the x-axis.
y_cutoff	Numeric, specifying cutoff of the y-axis.
mycolour	A color vector, specifying colors of non-significant, significantly up and down-regulated genes.
alpha	Numeric, parameter in ggplot.
force	Numeric, Parameter for geom_text_repel. Force of repulsion between overlapping text labels.
main	A character, specifying title.
xlab	A character, specifying title of x-axis.
ylab	A character, specifying title of y-axis.
filename	A character, specifying a file name to create on disk. Set filename to be "NULL", if don't want to save the figure.
width	Numeric, specifying width of figure.
height	Numeric, specifying height of figure.
...	Other available parameters in ggsave.

Value

An object created by ggplot, which can be assigned and further customized.

Author(s)

Wubing Zhang

Examples

file1 = file.path(system.file("extdata", package = "MAGeCKFlute"),
"testdata/rra.gene_summary.txt")
gdata = ReadRRA(file1)
VolcanoView(gdata, x = "Score", y = "FDR", Label = "id")

WubingZhang/MAGeCKFlute documentation built on Jan. 27, 2024, 2:43 p.m.