R: Plot a representation of the patterns and their frequencies

patternMap {MPFE}

R Documentation

Plot a representation of the patterns and their frequencies

Description

Plot the observed distribution and the estimated distribution of the methylation patterns

Usage

  patternMap(patterns,
             minFreq=0,
             maxFreq=1,
             noSpurious=TRUE,
             estimatedDistribution=TRUE,
             topDown=TRUE,
             allTicks=FALSE,
             methCol='black',
             unMethCol='white',
             ...)

Arguments

`patterns`	A data frame obtained from the output of the function `estimatePatterns`.
`minFreq`	Only plot patterns with at least `minFreq` frequency.
`maxFreq`	Only plot patterns with more `maxFreq` frequency or more.
`noSpurious`	Don't plot spurious patterns (only relevant if `estimatedDistribution` is `FALSE`).
`estimatedDistribution`	Use the frequencies from the estimated distribution. If `FALSE`, use the observed distribution.
`topDown`	Put the most abundant patterns at the top. If `FALSE` the most abundant patterns are at the bottom.
`allTicks`	Draw a tick under every position.
`methCol`	The colour for the methylated positions. Can be a single colour, a vector of colours (recycled), or a function (for instance from `colorRampPalette`).
`unMethCol`	As `methCol` but for un-methylated positions.
`...`	Other arguments passed to `plot`

Details

This function draws a map of the different pattern and their frequencies based on the values returned by estimatePatterns.

Author(s)

Peijie Lin, Sylvain Foret, Conrad Burden

Examples

  data(patternsExample)
  estimates <- estimatePatterns(patternsExample, 
                                epsilon=0.02, 
                                eta=0.01)
  patternMap(estimates[[1]])

[Package MPFE version 1.16.0 Index]