VolcanoView: Volcano View

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

Description

Volcano plot

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 = "Log2 Fold Change",
  ylab = "-Log10(Adjust.P)",
  filename = NULL,
  width = 4,
  height = 2.5,
  ...
)

Arguments

df	Data frame
x	Colname of df specifying x-axis in Volcanno figure, 'logFC' (default).
y	Colname of df specifying y-axis in Volcanno figure, 'adj.P.Val' (default), which will be plot after log10 transformation.
Label	Colname of df specifying labeled terms in Volcanno figure.
top	Interger, the number of top significant terms to be labeled.
topnames	Character vector, indicating interested terms to be labeled.
x_cutoff	Cutoff of x-axis.
y_cutoff	Cutoff of y-axis.
mycolour	A color vector, specifying colors of non-significant, significant up and down-regulated genes.
alpha	Parameter in ggplot.
force	Parameter for geom_text_repel.
main	Title of volcano figure.
xlab	Label of x-axis in figure.
ylab	Label of y-axis in figure.
filename	Figure file name to create on disk. Default filename="NULL", which means don't save the figure on disk.
width	Width of figure.
height	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")

MAGeCKFlute documentation built on Nov. 8, 2020, 5:40 p.m.