patternMap: Plot a representation of the patterns and their frequencies

In MPFE: Estimation of the amplicon methylation pattern distribution from bisulphite sequencing data

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]])

MPFE documentation built on Nov. 8, 2020, 7:49 p.m.