cloneTrack: Clone tracking plot

In elulu3/LymphoSeqTest: Analyze high-throughput sequencing of T and B cell receptors

Clone tracking plot

Description

Creates line plot tracking amino acid frequencies across multiple samples

Usage

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

Arguments

study_table	A tibble of productive amino acid sequences generated by LymphoSeq 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 (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 (default), will pull all junction_aa sequences from the sequence matrix.
unassigned

Details

The plot is made using the package ggplot2 and can be reformatted using ggplot2 functions. See examples below.

Value

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

See Also

An excellent resource for examples on how to reformat a ggplot can be found in the R Graphics Cookbook online (http://www.cookbook-r.com/Graphs/).

Examples

file_path <- system.file("extdata", "TCRB_sequencing", package = "LymphoSeq2")

stable <- readImmunoSeq(path = file_path)

atable <- productiveSeq(study_table = stable, aggregate = "junction_aa")

top_freq <- topFreq(atable, frequency = 0.001)

# Track clones without mapping or tracking specific sequences
cloneTrack(atable)

# Track top 20 clones mapping to the CD4 and CD8 samples
cloneTrack(atable, sample_list = c("TRB_CD4_949", "TRB_CD8_949"),
   sequence_track = top_freq$junction_aa[1:20], unassigned = TRUE) 

# Track the top 10 clones from top.freq
cloneTrack(study_table = atable, sequence_track = top_freq$junction_aa[1:10], 
           unassigned = FALSE) 

# Track clones mapping to the CD4 and CD8 samples while ignoring all others
cloneTrack(study_table = atable, sample_list = c("TRB_CD4_949", "TRB_CD8_949"),
   unassigned = FALSE) 

# Track clones mapping to the CD4 and CD8 samples and track 2 specific sequences
cloneTrack(study_table = atable, sample_list = c("TRB_CD4_949", "TRB_CD8_949"),
   sequence_track = c("CASSPPTGERDTQYF", "CASSQDRTGQYGYTF"), unassigned = FALSE)

elulu3/LymphoSeqTest documentation built on Aug. 27, 2022, 5:47 a.m.