commonSeqsVenn: Common sequences Venn diagram

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

Common sequences Venn diagram

Description

Creates a Venn diagram comparing the number of common sequences in two or three repertoire_ids.

Usage

commonSeqsVenn(repertoire_ids, amino_table)

Arguments

repertoire_ids	A character vector of two or three names of repertoire_ids in productiveSeq() table to compare.
amino_table	A tibble of amino acid sequences generated by the function productiveSeq().

Value

Returns a a Venn diagram of the number of common sequences between two or three repertoire_ids.

See Also

productiveSeq(), commonSeqs(), commonSeqsPlot(), commonSeqsBar()

Examples

file_path <- system.file("extdata", "TCRB_sequencing",
 package = "LymphoSeq2")
study_table <- LymphoSeq2::readImmunoSeq(path = file_path, threads = 1)
study_table <- LymphoSeq2::topSeqs(study_table, top = 100)
amino_table <- LymphoSeq2::productiveSeq(
  study_table = study_table,
  aggregate = "junction_aa"
)
# Plot a triple Venn diagram
LymphoSeq2::commonSeqsVenn(
  repertoire_ids = c(
    "TRB_Unsorted_0",
    "TRB_Unsorted_32", "TRB_Unsorted_83"
  ),
  amino_table = amino_table
)
# Plot a double Venn diagram
LymphoSeq2::commonSeqsVenn(repertoire_ids = c(
  "TRB_Unsorted_0",
  "TRB_Unsorted_32"
), amino_table = amino_table)

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