commonSeqsPlot {LymphoSeq} | R Documentation

## Common sequences plot

### Description

Creates a scatter plot of just the sequences in common between two samples.

### Usage

    commonSeqsPlot(sample1, sample2, productive.aa, show = "common")

### Arguments

`sample1` | A name of a sample in a list of data frames generated by the LymphoSeq function productiveSeq.
`sample2` | A name of a sample in a list of data frames generated by the LymphoSeq function productiveSeq.
`productive.aa` | A list of data frames of productive amino acid sequences produced by the LymphoSeq function productiveSeq containing the samples to be compared.
`show` | A character vector specifying whether only the common sequences should be shown or all sequences. Available options are "common" or "all".

### Details

The plot is made using the package ggplot2 and can be reformatted using ggplot2 functions. See examples below.

### Value

Returns a frequency scatter plot of two samples showing only the shared sequences.

### See Also

An excellent resource for examples on how to reformat a ggplot can be found in the R Graphics Cookbook online (http://www.cookbook-r.com/Graphs/).

### 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")

    commonSeqsPlot("TRB_Unsorted_32", "TRB_Unsorted_83",
       productive.aa = productive.aa)

    # Change the X and Y axises to log-10 scale
    commonSeqsPlot("TRB_Unsorted_32", "TRB_Unsorted_83",
       productive.aa = productive.aa) +
       ggplot2::scale_x_log10() +
       ggplot2::scale_y_log10() +
       ggplot2::annotation_logticks(sides = "bl")

[Package LymphoSeq version 1.20.0 Index]