report: Plots AbSeqRep or AbSeqCRep object to the specfied directory

In malhamdoosh/abseqR: Reporting and data analysis functionalities for Rep-Seq datasets of antibody libraries

Description

Plots all samples in the object argument and saves the analysis in outputDir. Users can optionally specify which samples in object should be compared. Doing so generates additional plots for clonotype comparison and the usual plots will also conveniently include these samples using additional aesthetics.

This method is analogous to abseqReport. The only difference is that this method accepts AbSeqRep or AbSeqCRep objects as its first parameter, and the outputDir specifies where to store the result.

Usage

report(object, outputDir, report = 3)

## S4 method for signature 'AbSeqRep'
report(object, outputDir, report = 3)

## S4 method for signature 'AbSeqCRep'
report(object, outputDir, report = 3)

Arguments

object	AbSeqRep or AbSeqCRep object to plot.
outputDir	string type. Directory where analysis will be saved to.
report	(optional) integer type. The possible values are: 0 - does nothing (returns named list of AbSeqRep objects) 1 - generates plots for csv files 2 - generates a report that collates all plots 3 - generates interactive plots in report (default) each value also does what the previous values do. For example, report = 2 will return a named list of AbSeqRep objects, plot csv files, and generate a (non-interactive)HTML report that collates all the plots together.

Value

named list. List of AbSeqRep objects. The names of the list elements are taken directly from the repertoire object itself. This return value is consistent with the return value of abseqReport.

See Also

abseqReport. Analogus function, but takes input from a string that signifies the output directory of abseqPy as the first arugment instead.

AbSeqRep

AbSeqCRep

Examples

# Use example data from abseqR as abseqPy's output, substitute this
# with your own abseqPy output directory
abseqPyOutput <- tempdir()
file.copy(system.file("extdata", "ex", package = "abseqR"), abseqPyOutput, recursive=TRUE)
samples <- abseqReport(file.path(abseqPyOutput, "ex"), report = 0)


# The provided example data has PCR1, PCR2, and PCR3 samples contained within
# We can use the + operator to combine samples, thus requesting the
# report function to compare them:
pcr12 <- samples[["PCR1"]] + samples[["PCR2"]]

# generate plots and report for this new comparison
# report(pcr12, "PCR1_vs_PCR2")

# generate plots only
# report(pcr12, "PCR1_vs_PCR2", report = 1)

# generate plots, and a non-interactive report
# report(pcr12, "PCR1_vs_PCR2", report = 2)

# generate plots, and an interactive report
# report(pcr12, "PCR1_vs_PCR2", report = 3)   # this is the default

malhamdoosh/abseqR documentation built on May 24, 2019, 12:36 a.m.