plot_dissimilarity_summary: An area plot summary of the different causes of column...

In TS404/AlikeAlignmentAligner: Comparison of Alternative Multiple Sequence Alignments

Description

An area plot summary of the different causes of column dissimilarity between two multiple sequence alignments

Usage

plot_dissimilarity_summary(x, scale = TRUE, stack = TRUE, display = TRUE)

Arguments

x	an object of type "pairwise alignment comparison" (typically the summary file generated by compare_alignments)
scale	scale data to proportion of characters that are not conserved gaps (default = TRUE)
stack	stacked area plot in stead of line plot (default = TRUE)
display	display this plot (default = TRUE)

Note

This function generates a detailed breakdown of the differences between the multiple sequence alignments for each column of the reference alignment. For each column, the relative proportions of merges, splits and shifts is plotted as a proportion of characters that are not merely conserved gaps.

Examples

data(reference_alignment)
data(comparison_alignment)
PAC <- compare_alignments(reference_alignment, comparison_alignment)
plot_dissimilarity_summary(PAC, stack=TRUE)

TS404/AlikeAlignmentAligner documentation built on Oct. 13, 2021, 4:13 p.m.