MAView {MAGeCKFlute} | R Documentation

## MAplot of gene beta scores

### Description

MAplot of gene beta scores in Control vs Treatment

### Usage

    MAView(
      beta,
      ctrlname = "Control",
      treatname = "Treatment",
      main = NULL,
      show.statistics = TRUE,
      add.smooth = TRUE,
      lty = 1,
      smooth.col = "red",
      plot.method = c("loess", "lm", "glm", "gam"),
      filename = NULL,
      width = 5,
      height = 4,
      ...
    )

### Arguments

`beta` | Data frame, including `ctrlname` and `treatname` as columns.
`ctrlname` | Character vector, specifying the name of control sample.
`treatname` | Character vector, specifying the name of treatment sample.
`main` | As in plot.
`show.statistics` | Show statistics .
`add.smooth` | Whether add a smooth line to the plot.
`lty` | Line type for smooth line.
`smooth.col` | Color of smooth line.
`plot.method` | A string specifying the method to fit smooth line, which should be one of "loess" (default), "lm", "glm" and "gam".
`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

### Examples

    file3 = file.path(system.file("extdata", package = "MAGeCKFlute"),
    "testdata/mle.gene_summary.txt")
    dd = ReadBeta(file3)
    MAView(dd, ctrlname = "dmso", treatname = "plx")

[Package MAGeCKFlute version 1.12.0 Index]