commonSeqsBar: Common sequences bar plot
In LymphoSeq: Analyze high-throughput sequencing of T and B cell receptors

Description Usage Arguments Value Examples

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.

1 2	commonSeqsBar(productive.aa, samples, color.sample = NULL, color.intersection = NULL, color = "#377eb8", labels = "no")

`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".

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

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")