rankPlot: Rankplot for given column.

In Tong-Chen/YSX: For Yishengxin Training

Description

Rankplot for given column.

Usage

rankPlot(
  data,
  order_col = "log2FoldChange",
  midpoint = 0,
  saveplot = NULL,
  label = NULL,
  alpha = 0.5,
  colorvector = c("green", "yellow", "red"),
  width = 13.5,
  height = 15,
  ...
)

Arguments

data	A dataframe with effective row names.
order_col	Specify which column would be used for plot. Default "log2FoldChange".
midpoint	Specify the midpoint for color show. Default 0.
saveplot	Save plot to given file "a.pdf", "b.png".
label	Label points. Accept a number to get top x points to label (both directions). Or a vector matched with rownames of dataframe to label specified points. Or a named vector to label specified points with new names.
alpha	Transparency value.
colorvector	A vector with length 2 to speicfy low and high colors. Or a vector with length 3 to specify low, middle and high colors. Default c("green","yellow","red").
width	Picture width in "cm".
height	Picture height in "cm".
...	Additional parameters given to pheatmap like "width", "height", .etc.

Value

A ggplot2 object

Examples

a <- data.frame(log2FoldChange=rnorm(1000), row.names=paste0("YSX",1:1000))

## Raw plot

rankPlot(a)

## Label top 10

rankPlot(a, label=10)

## Label specified points

rankPlot(a, label=c("YSX1","YSX2","YSX10"))

## Label specified points with new names

b <- c("A","B","C")
names(b) <- c("YSX1","YSX2","YSX10")
rankPlot(a, label=b)

Tong-Chen/YSX documentation built on Jan. 25, 2021, 2:49 a.m.