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

Description Usage Arguments Note Examples

View source: R/Plots.R

Description

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

Usage

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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)

Note

This function generates a plot that summarises the similarity between the two multiple sequence alignments for each column of the reference alignment. For each column, it plots the proportion of identical character matches as a proportion of the characters that are not merely conserved gaps. The overall average proportion of identical characters that are not conserved gaps is overlaid as a percentage. For alignments of cysteine-rich proteins, the cysteine abundance for each column may also be plotted to indicate columns containing conserved cysteines ('cys=TRUE').

Examples

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