Plot rarefication and extrapolation curves for samples — plotRarefactionCurve • LymphoSeqTest

Given a study table, for each sample plot rarefaction curves to estimate repertoire diversity. The method used to generate the rarefaction curve is derived from Chao et al., (2014) using the iNEXT library

Usage

plotRarefactionCurve(study_table)

Arguments

study_table: A tibble consisting antigen receptor sequencing data imported by the LymphoSeq function readImmunoSeq. "aminoAcid", "count", and "frequencyCount" are required columns.

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")