commonSeqsPlot {LymphoSeq} | R Documentation |
Creates a scatter plot of just the sequences in common between two samples.
commonSeqsPlot(sample1, sample2, productive.aa, show = "common")
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". |
The plot is made using the package ggplot2 and can be reformatted using ggplot2 functions. See examples below.
Returns a frequency scatter plot of two samples showing only the shared sequences.
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/).
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")