Plot Multiple Sequence Alignment using 'ggplot2'


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Documentation for package ‘ggmsa’ version 1.0.2

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available_colors List Color Schemes currently available
available_fonts List Font Families currently available
available_msa List MSA objects currently available
color_Clustal A color scheme of Culstal. The algorithm to assign colors for Multiple Sequence.
color_scheme Assigning colors to sequence alignment.
facet_msa segment MSA
geom_GC geom_GC
geom_helix geom_helix
geom_msa geom_msa
geom_msaBar geom_msaBar
geom_seed geom_seed
geom_seqlogo geom_seqlogo
get_consensus calling the consensus sequence.
gghelix gghelix
ggmsa ggmsa
ggSeqBundle ggSeqBundle
msa2tidy This function converts the msa_data to the tidy data.
plot plot method for SeqDiff object
plot-method plot method for SeqDiff object
readSSfile readSSfile
seqdiff seqdiff
SeqDiff-class show method
seqlogo seqlogo
show show method
show-method show method
simplot simplot
tidy_color cleaning the needless sequeces' color according to the consensus sequcence (only used in the consensus views).
tidy_msa tidy_msa