Visualize multiple sequence alignment of CDR3 sequences

Generate MSA alignment figures from the results of alignSeq()

Usage

plotAlignment(msa)

Arguments

msa

An msa object obtained from alignSeq() function in LymphoSeq2.

Value

Multiple sequence alignment plot.

See also

The function utilizes ggmsa package for visualizations. Further details on ggmsa can be found at the link mentioned below. https://cran.r-project.org/web/packages/ggmsa/vignettes/ggmsa.html

Examples

library(ggmsa)
#> Registered S3 methods overwritten by 'ggalt':
#>   method                  from   
#>   grid.draw.absoluteGrob  ggplot2
#>   grobHeight.absoluteGrob ggplot2
#>   grobWidth.absoluteGrob  ggplot2
#>   grobX.absoluteGrob      ggplot2
#>   grobY.absoluteGrob      ggplot2
#> ggmsa v1.3.4  Document: http://yulab-smu.top/ggmsa/
#> 
#> If you use ggmsa in published research, please cite:
#> L Zhou, T Feng, S Xu, F Gao, TT Lam, Q Wang, T Wu, H Huang, L Zhan, L Li, Y Guan, Z Dai*, G Yu* ggmsa: a visual exploration tool for multiple sequence alignment and associated data. Briefings in Bioinformatics. DOI:10.1093/bib/bbac222
file_path <- system.file("extdata", "IGH_sequencing", package = "LymphoSeq2")
study_table <- LymphoSeq2::readImmunoSeq(path = file_path, threads = 1)
study_table <- LymphoSeq2::topSeqs(study_table, top = 100)
nucleotide_table <- LymphoSeq2::productiveSeq(study_table,
 aggregate = "junction")
msa <- LymphoSeq2::alignSeq(nucleotide_table,
  repertoire_id = "IGH_MVQ92552A_BL",
  type = "junction_aa", method = "ClustalW"
)
#> use default substitution matrix
LymphoSeq2::plotAlignment(msa)
#> Coordinate system already present. Adding new coordinate system, which will
#> replace the existing one.