Description Usage Arguments Note Examples
A line plot summary of column similarity between two multiple sequence alignments
1 2 3 4 5 6 7 |
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) |
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').
1 2 3 4 | data(reference_alignment)
data(comparison_alignment)
PAC <- compare_alignments(reference_alignment, comparison_alignment, CS=TRUE)
plot_similarity_summary(PAC, CS=TRUE, cys=TRUE)
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