polarPlot {piano} | R Documentation

## Polar plot

### Description

Produces a Polar plot, mapping p-values to chromosome location. This function is used by `diffExp`.

### Usage

    polarPlot(pValues, chromosomeMapping, colors = c("red", "green", "blue",
      "yellow", "orange", "purple", "tan", "cyan", "gray60", "black"),
      save = FALSE, verbose = TRUE)

### Arguments

`pValues` | a `data.frame` containing p-values for different contrasts in different columns. Column names are used as contrast names. Maximum number of columns allowed are ten.
`chromosomeMapping` | character string giving the name of the chromosome mapping file, or an object of class `data.frame` or similar containing the chromosome mapping. See details below.
`colors` | character vector of colors to be used by the Polar plot.
`save` | should the figures be saved? Defaults to `FALSE`.
`verbose` | verbose? Defaults to `TRUE`.

### Details

This function is mainly used by `diffExp` but can also be used separately by the user.

The argument `chromosomeMapping` should be either a `data.frame` or a tab delimited text file and include the columns chromosome with the chromosome name and chromosome location containing the starting position of each gene. A `-` sign can be used to denote the antisense strand but this will be disregarded while plotting. The rownames should be probe IDs or, if using a text file, the first column with a column header should contain the probe IDs. If relying on an `ArrayData` object (called `arrayData`) and containing an `annotation` field, the `chromosomeMapping` can be set to `arrayData$annotation[,c(2,3)]` (see the example below).

The Polar plot sorts the genes according to chromosomal location, for each chromosome starting with unknown positions followed by increasing number in the chromosome location column. Genes which do not map to any chromosome are listed as U for unknown. The radial lines in the Polar plot are -log10 scaled p-values, so that a longer line means a smaller p-value. This gives an overview of the magnitude of differential expression for each contrast.

### Author(s)

Leif Varemo piano.rpkg@gmail.com and Intawat Nookaew piano.rpkg@gmail.com

### See Also

piano, `diffExp`, `radial.plot`

### Examples

      # Get path to example data and setup files:
      dataPath <- system.file("extdata", package="piano")

      # Load normalized data:
      myArrayData <- loadMAdata(datadir=dataPath, dataNorm="norm_data.txt.gz", platform="yeast2")

      # Perform differential expression analysis:
      pfc <- diffExp(myArrayData, plot=FALSE,
                     contrasts=c("aerobic_Clim - anaerobic_Clim",
                                 "aerobic_Nlim - anaerobic_Nlim"))

      # Get chromosome mapping from myArrayData:
      chrMap <- myArrayData$annotation[,c(2,3)]
      # Get p-values from pfc
      pval <- pfc$pValues
      # Draw the polar plot:
      polarPlot(pval, chromosomeMapping=chrMap)

[Package piano version 1.22.0 Index]