matchDistribution {CNEr} | R Documentation

## Plot the distribution of matched alignments.

### Description

Given a `Axt` alignment, plot a heatmap showing the percentage of each matched alignments.

### Usage

      matchDistribution(x, size=10000, title=NULL)

### Arguments

`x` | `Axt` object.
`size` | `integer`(1): the number of alignments to use. By default, it is 10000.
`title` | `character`(1): the customised title for the plot.

### Details

By default, if there are more than 10,000 alignments, 10,000 alignments will be sampled and calculated for the distribution for speed purposes.

Only the four bases (A, C, G, T), gap (-) and any (N) are displayed. Other ambiguous bases are not considered.

### Value

A ggplot2 object will be returned.

### Author(s)

Ge Tan

### Examples

      axtFile <- file.path(system.file("extdata", package="CNEr"),
                           "hg38.danRer10.net.axt")
      axt <- readAxt(axtFile)
      matchDistribution(axt)

[Package CNEr version 1.18.1 Index]