plot_similarity_heatmap: A heatmap plot of the column identities between two multiple...

In AlignStat: Comparison of Alternative Multiple Sequence Alignments

Description

A heatmap plot of the column identities between two multiple sequence alignments

Usage

plot_similarity_heatmap(x, scale = 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)
display	display this plot (default = TRUE)

Note

This function displays the similarity between each pairwise column comparison for the reference and comparison MSAs. Colour density is determined by the proportion of identical character matches between the columns, normalised to the number of characters that are not merely conserved gaps. This gives a representation of which columns are well agreed upon by the MSAs, and which columns are split by one MSA relative to the other.

Examples

data(reference_alignment)
data(comparison_alignment)
PAC <- compare_alignments(reference_alignment,comparison_alignment)
plot_similarity_heatmap(PAC)

AlignStat documentation built on May 30, 2017, 5:25 a.m.