matchDistribution: Plot the distribution of matched alignments.

Description Usage Arguments Details Value Author(s) Examples

Description

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

Usage

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  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

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

CNEr documentation built on Nov. 8, 2020, 5:36 p.m.