plotAlignment: Visualize multiple sequence alignment of CDR3 sequences

In shashidhar22/LymphoSeq2: Analyze high-throughput sequencing of T and B cell receptors

Visualize multiple sequence alignment of CDR3 sequences

Description

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)
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"
)
LymphoSeq2::plotAlignment(msa)

shashidhar22/LymphoSeq2 documentation built on Jan. 16, 2024, 4:29 a.m.