ggvolcano: Volcano plot by ggplot2

In yikeshu0611/TCGAimmunelncRNA: TCGAimmunelncRNA

Description

Volcano plot by ggplot2

Usage

ggvolcano(
  data,
  logFC = "logFC",
  pvalue = "PValue",
  symbol = NULL,
  pvalue.cutoff = 0.01,
  lgf = 2,
  alpha = 0.5,
  size = 2,
  colours = c("red", "blue", "gray"),
  size.border = 1,
  size.vhline = 0.75,
  size.axis.text = 13,
  size.axis.title = 14,
  size.symbol = 4,
  ticks.length = 0.15,
  ticks.width = 1,
  legend.text = c("Up", "Down", "NS"),
  legend.title = NULL,
  legend.position = "right",
  size.legend.text = 12,
  size.legend.title = 15,
  symbol.pvalue.cutoff = NULL,
  symbol.lgf = NULL,
  cat = TRUE,
  flip = FALSE,
  grid = FALSE
)

Arguments

data	results of difference expression genes, which must contains logFC and p value.
logFC	default is logFC
pvalue	default if PValue
symbol	default if NULL
pvalue.cutoff	default is 0.01
lgf	default is 2
alpha	for points, default is 0.5
size	for points, default is 2
colours	for points, default is red, bule and gray
size.border	1
size.vhline	0.75
size.axis.text	13
size.axis.title	14
size.symbol	4
ticks.length	0.15
ticks.width	1
legend.text	text for three groups, default is Up, Down and NS. NS means not significant
legend.title	NULL
legend.position	legend position, which can be right, left, top, bottom, or two of them. Or two numbers, eg: c(1,1)
size.legend.text	12
size.legend.title	15
symbol.pvalue.cutoff	default is NULL, which takes value of pvalue.cutoff
symbol.lgf	default is NULL, which takes value of lgf
cat	logical, whether to output gene number for three classifications.
flip	logical, default is TRUE, whether to flip coordinate
grid	logical, default is FALSE, whether to show panel grid

Value

one ggplot2 volcano picture

yikeshu0611/TCGAimmunelncRNA documentation built on Dec. 23, 2021, 7:20 p.m.