matchDistribution: Plot the distribution of matched alignments.

In ge11232002/CNEr: CNE Detection and Visualization

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)

ge11232002/CNEr documentation built on Oct. 26, 2022, 7:08 p.m.