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% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/plots.R
\name{vis.shared.clonotypes}
\alias{vis.shared.clonotypes}
\title{Visualisation of shared clonotypes occurrences among repertoires.}
\usage{
vis.shared.clonotypes(
.shared.rep,
.x.rep = NA,
.y.rep = NA,
.title = NA,
.ncol = 3,
.point.size.modif = 1,
.cut.axes = T,
.density = T,
.lm = T,
.radj.size = 3.5,
.plot = T
)
}
\arguments{
\item{.shared.rep}{Shared repertoires, as from \link{shared.repertoire} function.}
\item{.x.rep}{Which repertoire show on x-axis. Either a name or an index of a repertoire
in the \code{.shared.rep} or NA to choose all repertoires.}
\item{.y.rep}{Which repertoire show on y-axis. Either a name or an index of a repertoire
in the \code{.shared.rep} or NA to choose all repertoires.}
\item{.title}{Main title of the plot.}
\item{.ncol}{Number of columns in the resulting plot.}
\item{.point.size.modif}{Modify this to correct sizes of points.}
\item{.cut.axes}{If T than cut axes' limits to show only frequencies that exists.}
\item{.density}{If T than plot densities of shared and unique clonotypes.}
\item{.lm}{If T than fit and plot a linear model to shared clonotypes.}
\item{.radj.size}{Size of the text for R^2-adjusted.}
\item{.plot}{If F than return grobs instead of plotting.}
}
\value{
ggplot2 object or plot
}
\description{
Visualise counts or proportions of shared clonotypes among repertoires.
Code adapted from https://www.r-bloggers.com/ggplot2-cheatsheet-for-visualizing-distributions/.
}
\examples{
\dontrun{
data(twb)
# Show shared nucleotide clonotypes of all possible pairs
# using the Read.proportion column
twb.sh <- shared.repertoire(twb, "n0rp")
vis.shared.clonotypes(twb.sh, .ncol = 4)
# Show shared amino acid + Vseg clonotypes of pairs
# including the Subj.A (the first one) using
# the Read.count column.
twb.sh <- shared.repertoire(twb, "avrc")
vis.shared.clonotypes(twb.sh, 1, NA, .ncol = 4)
# same, just another order of axis
vis.shared.clonotypes(twb.sh, NA, 1, .ncol = 4)
# Show shared nucleotide clonotypes of Subj.A (the first one)
# Subj.B (the second one) using the Read.proportion column.
twb.sh <- shared.repertoire(twb, "n0rp")
vis.shared.clonotypes(twb.sh, 1, 2)
# Show the same plot, but with much larget points.
vis.shared.clonotypes(twb.sh, 1, 2, .point.size.modif = 3)
}
}
\seealso{
\link{shared.repertoire}
}
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