matchDistribution: Plot the distribution of matched alignments.
In CNEr: CNE Detection and Visualization

Description Usage Arguments Details Value Author(s) Examples

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

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

`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.

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.

A ggplot2 object will be returned.

Ge Tan

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