ScatterView {MAGeCKFlute}R Documentation

Scatter plot

Description

Scatter plot of all genes, in which x-axis is mean beta score in Control samples, y-axis is mean beta scores in Treatment samples.

Usage

ScatterView(beta, ctrlname = "Control", treatname = "Treatment",
  scale_cutoff = 1, main = NULL, filename = NULL, width = 5,
  height = 4, ...)

Arguments

beta

Data frame, including ctrlname and treatname as columns.

ctrlname

A character, specifying the names of control samples.

treatname

A character, specifying the names of treatment samples.

scale_cutoff

Boolean or numeric, whether scale cutoff to whole genome level, or how many standard deviation will be used as cutoff.

main

As in 'plot'.

filename

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

width

As in ggsave.

height

As in ggsave.

...

Other available parameters in function 'ggsave'.

Value

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

Author(s)

Wubing Zhang

See Also

SquareView

Examples

data(MLE_Data)
# Read beta score from gene summary table in MAGeCK MLE results
dd = ReadBeta(MLE_Data, organism="hsa")
ScatterView(dd, ctrlname = "D7_R1", treatname = "PLX7_R1")



[Package MAGeCKFlute version 1.0.1 Index]