VolcanoView {MAGeCKFlute}R Documentation

Volcano View

Description

Volcano plot

Usage

VolcanoView(df, x = "logFC", y = "adj.P.Val", Label = NA, top = 5,
  topnames = NULL, filename = NULL, x_cutoff = log2(1.5),
  y_cutoff = 0.05, main = NULL, xlab = "Log2 Fold Change",
  ylab = "-Log10(Adjust.P)", ...)

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).

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.

filename

Figure file name to create on disk. Default filename="NULL", which means don't save the figure on disk.

x_cutoff

Cutoff of x-axis.

y_cutoff

Cutoff of y-axis.

main

Title of volcano figure.

xlab

Label of x-axis in figure.

ylab

Label of y-axis in figure.

...

Other available parameters in ggsave.

Value

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

Author(s)

Wubing Zhang

Examples

data(rra.gene_summary)
rra = ReadRRA(rra.gene_summary)
VolcanoView(rra, x = "LFC", y = "FDR", Label = "Official")


[Package MAGeCKFlute version 1.2.3 Index]