cloneTrack: Clone tracking line plot

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

Clone tracking line plot

Description

Creates line plot tracking amino acid frequencies across multiple samples

Usage

cloneTrack(study_table, sample_list = NULL, sequence_track = NULL)

Arguments

study_table	A tibble of productive amino acid sequences generated by LymphoSeq2 function productiveSeq() where the aggregate parameter was set to "junction_aa"
sample_list	A character vector of one or more repertoire_ids to track. If set to NULL (the default), all repertoire_ids in the sequence matrix will be tracked.
sequence_track	An optional character vector of one or more amino acid sequences to track. If set to NULL (the default), will pull all junction_aa sequences from the sequence matrix.

Value

Returns a line plot showing the amino acid frequencies across multiple samples in the sequence matrix where each line represents one unique sequence.

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"
)
top_freq <- LymphoSeq2::topFreq(amino_table, frequency = 0.001)
# Track clones without mapping or tracking specific sequences
LymphoSeq2::cloneTrack(amino_table)
# Track top 20 clones mapping to the CD4 and CD8 samples
LymphoSeq2::cloneTrack(amino_table,
  sample_list = c("TRB_CD4_949", "TRB_CD8_949"),
  sequence_track = top_freq$junction_aa[1:20]
)
# Track the top 10 clones from top.freq
LymphoSeq2::cloneTrack(
  study_table = amino_table,
  sequence_track = top_freq$junction_aa[1:10]
)
# Track clones mapping to the CD4 and CD8 samples while ignoring all others
LymphoSeq2::cloneTrack(
  study_table = amino_table,
  sample_list = c("TRB_CD4_949", "TRB_CD8_949")
)
# Track clones mapping to the CD4 and CD8 samples and track 2 specific 
#sequences
LymphoSeq2::cloneTrack(
  study_table = amino_table, sample_list = c("TRB_CD4_949", "TRB_CD8_949"),
  sequence_track = c("CASSPPTGERDTQYF", "CASSQDRTGQYGYTF")
)

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