commonSeqsBar {LymphoSeq} | R Documentation

## Common sequences bar plot

### Description

Creates an UpSetR bar plot showing the number of intersecting sequences across multiple samples. This function is useful when more than 3 samples are being compared.

### Usage

    commonSeqsBar(productive.aa, samples, color.sample = NULL,
      color.intersection = NULL, color = "#377eb8", labels = "no")

### Arguments

`productive.aa` | A list data frames of of productive amino acid sequences generated by LymphoSeq function productiveSeq where the aggregate parameter was set to "aminoAcid".
`samples` | The names of two or more samples in the productive.aa list whose intersections will shown.
`color.sample` | The name of a single sample in the productive.aa list whose sequences will be colored in all samples that they appear in.
`color.intersection` | The names of two or more samples in the productive.aa list whose intersections will be colored.
`color` | A character vector of a color name that will be used highlight a selected sample or multiple sample intersections.
`labels` | A character vector indicating whether the number of intersecting sequences should be shown on the tops of the bars. Options include "yes" or "no".

### Value

Returns an UpSetR bar plot showing the number of intersecting sequences across multiple samples.

### Examples

    file.path <- system.file("extdata", "TCRB_sequencing", package = "LymphoSeq")

    file.list <- readImmunoSeq(path = file.path)

    productive.aa <- productiveSeq(file.list = file.list, aggregate = "aminoAcid")

    commonSeqsBar(productive.aa = productive.aa, samples = c("TRB_CD4_949", "TRB_CD8_949",
    "TRB_Unsorted_949", "TRB_Unsorted_1320"), color.sample = "TRB_CD8_949")

[Package LymphoSeq version 1.12.0 Index]