Common sequences plot

Creates a scatter plot of just the sequences in common between two samples.

Usage

commonSeqsPlot(sample1, sample2, productive_aa, show = "common")

Arguments

sample1

A name of a repertoire_id in a list of data frames generated by the LymphoSeq function productiveSeq.

sample2

A name of a repertoire_id in a list of data frames generated by the LymphoSeq function productiveSeq.

productive_aa

A tibble of productive amino acid sequences produced by the LymphoSeq function productiveSeq containing the samples to be compared.

show

A character vector specifying whether only the common sequences should be shown or all sequences. Available options are "common" or "all".

Value

Returns a frequency scatter plot of two samples showing only the shared sequences.

Details

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

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/).

commonSeqs

Examples

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

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

commonSeqsPlot("TRB_Unsorted_32", "TRB_Unsorted_83", 
   productive_aa = atable)


# Change the X and Y axis to log-10 scale
commonSeqsPlot("TRB_Unsorted_32", "TRB_Unsorted_83", 
   productive_aa = atable) +
   ggplot2::scale_x_log10() + 
   ggplot2::scale_y_log10() + 
   ggplot2::annotation_logticks(sides = "bl")