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ggmsa (version 1.0.2)

Plot Multiple Sequence Alignment using 'ggplot2'

Description

Supports visualizing multiple sequence alignment of DNA and protein sequences using 'ggplot2'. It supports a number of colour schemes, including Chemistry, Clustal, Shapely, Taylor and Zappo. Multiple sequence alignment can easily be combined with other 'ggplot2' plots, such as aligning a phylogenetic tree produced by 'ggtree' with multiple sequence alignment.

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Version

Install

install.packages('ggmsa')

Monthly Downloads

12

Version

1.0.2

License

Artistic-2.0

Maintainer

Guangchuang Yu

Last Published

August 3rd, 2021

Functions in ggmsa (1.0.2)

color_scheme

Assigning colors to sequence alignment.
geom_GC

geom_GC
facet_msa

segment MSA
geom_msa

geom_msa
available_msa

List MSA objects currently available
color_Clustal

A color scheme of Culstal. The algorithm to assign colors for Multiple Sequence.
available_colors

List Color Schemes currently available
readSSfile

readSSfile
simplot

simplot
seqdiff

seqdiff
gghelix

gghelix
get_consensus

calling the consensus sequence.
ggSeqBundle

ggSeqBundle
plot

plot method for SeqDiff object
geom_msaBar

geom_msaBar
msa2tidy

This function converts the msa_data to the tidy data.
show

show method
seqlogo

seqlogo
tidy_color

cleaning the needless sequeces' color according to the consensus sequcence (only used in the consensus views).
tidy_msa

tidy_msa
ggmsa

ggmsa
geom_seed

geom_seed
geom_seqlogo

geom_seqlogo
geom_helix

geom_helix
available_fonts

List Font Families currently available