AlignStat (version 1.3.1)

plot_similarity_summary: A line plot summary of column similarity between two multiple sequence alignments

Description

A line plot summary of column similarity between two multiple sequence alignments

Usage

plot_similarity_summary(x, scale = TRUE, CS = FALSE, cys = FALSE, 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)

CS

additionally indicate columns with 100 percent identity using markers on the x-axis (default = FALSE)

cys

additionally show the cysteine abundance for each column (default = FALSE)

display

display this plot (default = TRUE)

Examples

data(reference_alignment)
data(comparison_alignment)
PAC <- compare_alignments(reference_alignment, comparison_alignment, CS=TRUE)
plot_similarity_summary(PAC, CS=TRUE, cys=TRUE)