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Last data update: 2014.03.03

R: Plot a representation of the patterns and their frequencies

patternMap

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]])

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(MPFE)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/MPFE/patternMap.Rd_%03d_medium.png", width=480, height=480)
> ### Name: patternMap
> ### Title: Plot a representation of the patterns and their frequencies
> ### Aliases: patternMap
> 
> ### ** Examples
> 
>   data(patternsExample)
>   estimates <- estimatePatterns(patternsExample, 
+                                 epsilon=0.02, 
+                                 eta=0.01)
>   patternMap(estimates[[1]])
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>