A line plot summary of sum of pairs score between two multiple sequence alignments

Description

A line plot summary of sum of pairs score between two multiple sequence alignments

Usage

plot_SP_summary(x, CS = TRUE, display = TRUE)

Arguments

Note

This function generates a plot that summarises the columnwise sums of pairs for the two multiple sequence alignments. For each column of the comparison alignment, it plots the proportion of conserved residue pairs as a proportion of the poassible residue pairs. The overall sum of pairs score, reverse sum of pairs score, and column score are also reported as percentages.

Examples

data(reference_alignment)
data(comparison_alignment)
PAC <- compare_alignments(reference_alignment,comparison_alignment,SP=TRUE)
plot_SP_summary(PAC)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(AlignStat)
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/AlignStat/plot_SP_summary.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plot_SP_summary
> ### Title: A line plot summary of sum of pairs score between two multiple
> ###   sequence alignments
> ### Aliases: plot_SP_summary
> 
> ### ** Examples
> 
> data(reference_alignment)
> data(comparison_alignment)
> PAC <- compare_alignments(reference_alignment,comparison_alignment,SP=TRUE)
> plot_SP_summary(PAC)
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>