plotBestNormal {PureCN} | R Documentation

## Plot the PCA of tumor and its best normal(s)

### Description

This function can be used to understand how a best normal is chosen by the `findBestNormal` function. It can be also used to tune the best normal selection by finding good parameter values for `num.normals` and `pcs`.

### Usage

    plotBestNormal(normal.coverage.files, tumor.coverage.file, normalDB, x = 1,
      y = 2, col.tumor = "red", col.best.normal = "blue",
      col.other.normals = "black", ...)

### Arguments

`normal.coverage.files` | Coverage file names of normal samples, typically identified via `findBestNormal`.
`tumor.coverage.file` | Coverage file or data of a tumor sample.
`normalDB` | Database of normal samples, created with `createNormalDatabase`.
`x` | Principal component (PC) to be plotted on x-axis.
`y` | PC to be plotted on y-axis.
`col.tumor` | Color of tumor in plot.
`col.best.normal` | Color of best normals in plot.
`col.other.normals` | Color of other normals in plot.
`...` | Arguments passed to the `plot` function.

### Value

Returns `NULL`.

### Author(s)

Markus Riester

### See Also

`createNormalDatabase findBestNormal`

### Examples

    normal.coverage.file <- system.file("extdata", "example_normal.txt",
        package="PureCN")
    normal2.coverage.file <- system.file("extdata", "example_normal2.txt",
         package="PureCN")
    normal.coverage.files <- c(normal.coverage.file, normal2.coverage.file)
    normalDB <- createNormalDatabase(normal.coverage.files)

    tumor.coverage.file <- system.file("extdata", "example_tumor.txt",
        package="PureCN")
    best.normal.coverage.file <- findBestNormal(tumor.coverage.file, normalDB)
    plotBestNormal(best.normal.coverage.file, tumor.coverage.file, normalDB)

    # Display sample sex. The first point in the plot is always tumor.
    plotBestNormal(best.normal.coverage.file, tumor.coverage.file, normalDB,
        pch=c(1,ifelse(normalDB$sex=="F", 1, 2)))

[Package PureCN version 1.8.1 Index]