commonSeqsBar: Common sequences bar plot

In davidcoffey/LymphoSeq: Analyze high-throughput sequencing of T and B cell receptors

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")

davidcoffey/LymphoSeq documentation built on Dec. 31, 2019, 9:52 p.m.