commonSeqsBar: Common sequences bar plot

Description Usage Arguments Value Examples

View source: R/commonSeqsBar.R

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

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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

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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")

LymphoSeq documentation built on Nov. 1, 2018, 3:54 a.m.