Plot Multiple Sequence Alignment using 'ggplot2'


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Documentation for package ‘ggmsa’ version 1.10.0

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adjust_ally adjust_ally
assign_dms assign_dms
available_colors List Color Schemes currently available
available_fonts List Font Families currently available
available_msa List MSA objects currently available
extract_seq extract_seq
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
gghelix gghelix
ggmaf ggmaf
ggmsa ggmsa
ggSeqBundle ggSeqBundle
Gram-negative_AKL.fasta Gram-negative_AKL
Gram-positive_AKL.fasta Gram-positive_AKL
GVariation GVariation
LeaderRepeat_All.fa A sample DNA alignment sequences
merge_seq merge_seq
plot plot method for SeqDiff object
plot-method plot method for SeqDiff object
readSSfile readSSfile
read_maf read_maf
reset_pos reset_pos
Rfam Rfam
sample.fasta A sample data used in ggmsa
seedSample.fa microRNA data used in ggmsa
seqdiff seqdiff
SeqDiff-class show method
seqlogo seqlogo
sequence-link-tree.fasta sequence-link-tree
show show method
show-method show method
simplify_hdata simplify_hdata
simplot simplot
theme_msa theme_msa
tidy_hdata tidy_hdata
tidy_maf_df tidy_maf_df
tidy_msa tidy_msa
tp53.fa TP53 MSA
TP53_genes.xlsx genome locus
treeMSA_plot treeMSA_plot