For sequence annotations, ggmsa supports individual modules to annotate sequence alignments. Annotated modules can be called by a
+ prefix. Automatically generated annotations that containing colored labels and symbols are overlaid on MSAs to indicate potentially conserved or divergent regions.
|geom_seqlogo()||geometric layer||automatically generated sequence logos for a MSA|
|geom_GC()||annotation module||shows GC content with bubble chart|
|geom_seed()||annotation module||highlights seed region on miRNA sequences|
|geom_msaBar()||annotation module||shows sequences conservation by a bar chart|
|geom_helix()||annotation module||depicts RNA secondary structure as arc diagrams(need extra data)|
Protein sequence logos annotation for MSA. Sequence logos play a major role in visualizing DNA, RNA and protein binding sites. In the following example,
geom_seqlogo() module is used to display sequence logos between 300 and 350 sites. The
+ can be used to link main function
ggmsa(protein_sequences, 300, 350, char_width = 0.5, seq_name = TRUE) + geom_seqlogo(color = "Chemistry_AA")
geom_GC() module calculating the GC-content in DNA/RNA sequences. The sizes of bubbles are identical with GC-content.
nt_sequence <- system.file("extdata", "LeaderRepeat_All.fa", package = "ggmsa") ggmsa(nt_sequence,font = NULL, color = "Chemistry_NT") + geom_seqlogo(color = "Chemistry_NT") + geom_GC() + theme(legend.position = "none")
geom_seed() helps to identify microRNA seed region by asterisks or shaded area. The seed region is a conserved heptameric sequence that is mostly situated at positions 2-7 from the miRNA 5´-end.
geom_msaBar shows the highest frequency of amino acid residues at each position by a bar chart.
ggmsa supports plotting RNA secondary structure as arc diagram by reference to R4RNA. For example, adding a structure arc above diagram multiple sequence alignment helps to identify the base pair conservation and co-variation.
known_file <- system.file("extdata", "vienna.txt", package = "R4RNA") known <- readSSfile(known_file, type = "Vienna" ) cripavirus_msa <- system.file("extdata", "Cripavirus.fasta", package = "ggmsa") ggmsa(cripavirus_msa, font = NULL, color = "Chemistry_NT", seq_name = FALSE, show.legend = TRUE, border = "white") + geom_helix(helix_data = known)