lorenzCurve: Lorenz curve
In LymphoSeq: Analyze high-throughput sequencing of T and B cell receptors

Description Usage Arguments Details Value See Also Examples

Plots a Lorenz curve derived from the frequency of the amino acid sequences.

1	lorenzCurve(samples, list)

`samples`	A character vector of sample names in list.
`list`	A list data frames generated using the LymphoSeq function readImmunoSeq or productiveSeq. "frequencyCount" is a required column.

The Gini coefficient is an alternative metric used to calculate repertoire diversity and is derived from the Lorenz curve. The Lorenz curve is drawn such that x-axis represents the cumulative percentage of unique sequences and the y-axis represents the cumulative percentage of reads. A line passing through the origin with a slope of 1 reflects equal frequencies of all sequences. The Gini coefficient is the ratio of the area between the line of equality and the observed Lorenz curve over the total area under the line of equality.

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

Returns a Lorenz curve.

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)

lorenzCurve(samples = names(file.list), list = file.list)

productive.aa <- productiveSeq(file.list = file.list, aggregate = "aminoAcid")

lorenzCurve(samples = names(productive.aa), list = productive.aa)

# Change the legend labels, line colors, and add a title
samples <- c("TRB_Unsorted_0", "TRB_Unsorted_32", 
   "TRB_Unsorted_83", "TRB_Unsorted_949", "TRB_Unsorted_1320")

lorenz.curve <- lorenzCurve(samples = samples, list = productive.aa)

labels <- c("Day 0", "Day 32", "Day 83", "Day 949", "Day 1320")

colors <- c("navyblue", "red", "darkgreen", "orange", "purple")

lorenz.curve + ggplot2::scale_color_manual(name = "Samples", breaks = samples, 
   labels = labels, values = colors) + ggplot2::ggtitle("Figure Title")

Loading required package: LymphoSeqDB
Registered S3 method overwritten by 'treeio':
  method     from
  root.phylo ape 
sh: 1: wc: Permission denied
Could not detect number of cores, defaulting to 1.

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Scale for 'colour' is already present. Adding another scale for 'colour',
which will replace the existing scale.
Warning message:
system call failed: Cannot allocate memory