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

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

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]