Plot clone

Creates alluvial tracking amino acid frequencies across multiple samples

Usage

plotTrack(
  clone_table,
  alist = NULL,
  apal = NULL,
  breaks = 2,
  alphas = 0,
  breaks_pal = c("#7fc97f", "#beaed4")
)

Arguments

clone_table

A tibble of productive amino acid sequences generated by LymphoSeq function cloneTrack

alist

An optional list of amino acid, if a list is provided only those sequences will be highlighted

apal

An optional list of palatte colors used for the amino acids to be highlighted

breaks

Add an additional band behind the alluvial plot to highligh group, specificies after which bar the break should appear

alphas

Set alpha for the band

breaks_pal

Specify palette for the bands

Value

An alluvial diagram tracking particular clone across samples.

Details

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

Examples

file_path <- system.file("extdata", "TCRB_sequencing", package = "LymphoSeqTest")
stable <- LymphoSeqTest::readImmunoSeq(path = file_path)
#> Rows: 1 Columns: 144
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: ","
#> chr (69): sequence_id, sequence, sequence_aa, locus, v_call, d_call, d2_call...
#> dbl (70): v_score, v_identity, v_support, d_score, d_identity, d_support, d2...
#> lgl  (5): rev_comp, productive, vj_in_frame, stop_codon, complete_vdj
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
#> Rows: 1000 Columns: 52
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: "\t"
#> chr (33): nucleotide, aminoAcid, vMaxResolved, vFamilyName, vGeneName, vGene...
#> dbl (15): count (templates/reads), frequencyCount (%), cdr3Length, vDeletion...
#> lgl  (4): vFamilyTies, jFamilyTies, jGeneNameTies, jGeneAlleleTies
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
#> Joining, by = c("sequence", "sequence_aa", "v_call", "d_call", "d2_call",
#> "j_call", "junction", "junction_aa", "duplicate_count", "clone_id",
#> "repertoire_id")
#> Rows: 1000 Columns: 52
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: "\t"
#> chr (34): nucleotide, aminoAcid, vMaxResolved, vFamilyName, vGeneName, vGene...
#> dbl (15): count (templates/reads), frequencyCount (%), cdr3Length, vDeletion...
#> lgl  (3): jFamilyTies, jGeneNameTies, jGeneAlleleTies
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
#> Joining, by = c("sequence", "sequence_aa", "v_call", "d_call", "d2_call",
#> "j_call", "junction", "junction_aa", "duplicate_count", "clone_id",
#> "repertoire_id")
#> Rows: 414 Columns: 52
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: "\t"
#> chr (34): nucleotide, aminoAcid, vMaxResolved, vFamilyName, vGeneName, vGene...
#> dbl (15): count (templates/reads), frequencyCount (%), cdr3Length, vDeletion...
#> lgl  (3): jFamilyTies, jGeneNameTies, jGeneAlleleTies
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
#> Joining, by = c("sequence", "sequence_aa", "v_call", "d_call", "d2_call",
#> "j_call", "junction", "junction_aa", "duplicate_count", "clone_id",
#> "repertoire_id")
#> Rows: 1000 Columns: 52
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: "\t"
#> chr (34): nucleotide, aminoAcid, vMaxResolved, vFamilyName, vGeneName, vGene...
#> dbl (15): count (templates/reads), frequencyCount (%), cdr3Length, vDeletion...
#> lgl  (3): jFamilyTies, jGeneNameTies, jGeneAlleleTies
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
#> Joining, by = c("sequence", "sequence_aa", "v_call", "d_call", "d2_call",
#> "j_call", "junction", "junction_aa", "duplicate_count", "clone_id",
#> "repertoire_id")
#> Rows: 1000 Columns: 52
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: "\t"
#> chr (34): nucleotide, aminoAcid, vMaxResolved, vFamilyName, vGeneName, vGene...
#> dbl (15): count (templates/reads), frequencyCount (%), cdr3Length, vDeletion...
#> lgl  (3): jFamilyTies, jGeneNameTies, jGeneAlleleTies
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
#> Joining, by = c("sequence", "sequence_aa", "v_call", "d_call", "d2_call",
#> "j_call", "junction", "junction_aa", "duplicate_count", "clone_id",
#> "repertoire_id")
#> Rows: 1000 Columns: 52
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: "\t"
#> chr (35): nucleotide, aminoAcid, vMaxResolved, vFamilyName, vGeneName, vGene...
#> dbl (15): count (templates/reads), frequencyCount (%), cdr3Length, vDeletion...
#> lgl  (2): jFamilyTies, jGeneAlleleTies
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
#> Joining, by = c("sequence", "sequence_aa", "v_call", "d_call", "d2_call",
#> "j_call", "junction", "junction_aa", "duplicate_count", "clone_id",
#> "repertoire_id")
#> Rows: 920 Columns: 52
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: "\t"
#> chr (29): nucleotide, aminoAcid, vMaxResolved, vFamilyName, vGeneName, vFami...
#> dbl (14): count (templates/reads), frequencyCount (%), cdr3Length, vDeletion...
#> lgl  (9): vGeneAllele, vGeneAlleleTies, dGeneAllele, dFamilyTies, dGeneAllel...
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
#> Joining, by = c("sequence", "sequence_aa", "v_call", "d_call", "d2_call",
#> "j_call", "junction", "junction_aa", "duplicate_count", "clone_id",
#> "repertoire_id")
#> Rows: 1000 Columns: 52
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: "\t"
#> chr (29): nucleotide, aminoAcid, vMaxResolved, vFamilyName, vGeneName, vFami...
#> dbl (14): count (templates/reads), frequencyCount (%), cdr3Length, vDeletion...
#> lgl  (9): vGeneAllele, vGeneAlleleTies, dGeneAllele, dFamilyTies, dGeneAllel...
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
#> Joining, by = c("sequence", "sequence_aa", "v_call", "d_call", "d2_call",
#> "j_call", "junction", "junction_aa", "duplicate_count", "clone_id",
#> "repertoire_id")
#> Rows: 1000 Columns: 52
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: "\t"
#> chr (29): nucleotide, aminoAcid, vMaxResolved, vFamilyName, vGeneName, vFami...
#> dbl (14): count (templates/reads), frequencyCount (%), cdr3Length, vDeletion...
#> lgl  (9): vGeneAllele, vGeneAlleleTies, dGeneAllele, dFamilyTies, dGeneAllel...
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
#> Joining, by = c("sequence", "sequence_aa", "v_call", "d_call", "d2_call",
#> "j_call", "junction", "junction_aa", "duplicate_count", "clone_id",
#> "repertoire_id")
#> Rows: 1000 Columns: 52
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: "\t"
#> chr (34): nucleotide, aminoAcid, vMaxResolved, vFamilyName, vGeneName, vGene...
#> dbl (15): count (templates/reads), frequencyCount (%), cdr3Length, vDeletion...
#> lgl  (3): jFamilyTies, jGeneNameTies, jGeneAlleleTies
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
#> Joining, by = c("sequence", "sequence_aa", "v_call", "d_call", "d2_call",
#> "j_call", "junction", "junction_aa", "duplicate_count", "clone_id",
#> "repertoire_id")
atable <- LymphoSeqTest::productiveSeq(stable, aggregate = "junction_aa")
ctable <- LymphoSeqTest::cloneTrack(study_table = atable,
                                sample_list = c("TRB_CD8_949", "TRB_CD8_CMV_369"))
LymphoSeqTest::plotTrack(ctable)