plot.HTPSpline.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/fitSpline.R
\name{plot.HTPSpline}
\alias{plot.HTPSpline}
\title{Plot the results of a fitted spline.}
\usage{
\method{plot}{HTPSpline}(
  x,
  ...,
  plotType = c("predictions", "derivatives", "derivatives2"),
  genotypes = NULL,
  plotIds = NULL,
  title = NULL,
  output = TRUE,
  outFile = NULL,
  outFileOpts = NULL
)
}
\arguments{
\item{x}{An object of class \code{HTPSpline}.}

\item{...}{Ignored.}

\item{plotType}{A character string indicating which spline component
should be plotted, either predictions, derivatives or second derivatives
("derivatives2").}

\item{genotypes}{A character vector indicating the genotypes for which
spline components should be plotted.}

\item{plotIds}{A character vector indicating the plotIds for which spline
components should be plotted.}

\item{title}{A character string used as title for the plot. If \code{NULL} a
default title is added to the plot depending on \code{plotType}.}

\item{output}{Should the plot be output to the current device? If
\code{FALSE} only a (list of) ggplot object(s) is invisibly returned. Ignored if
\code{outFile} is specified.}

\item{outFile}{A character string indicating the .pdf file to which the
plots should be written. If \code{NULL}, no file is written.}

\item{outFileOpts}{A named list of extra options for the pdf outfile, e.g.
width and height. See \code{\link[grDevices]{pdf}} for all possible options.}
}
\value{
A list of object of class ggplot is invisibly returned.
}
\description{
Plot the results of a fitted spline.
}
\examples{
## The data from the Phenovator platform have been corrected for spatial
## trends and outliers for single observations have been removed.

## Fit P-Splines on a subset of genotypes
subGeno <- c("G070", "G160")
fit.spline <- fitSpline(inDat = spatCorrectedVator,
                        trait = "EffpsII_corr",
                        genotypes = subGeno,
                        knots = 50)

## Visualize the P-Spline predictions for one genotype.
plot(fit.spline, genotypes = "G160")

## Visualize the first and second derivatives of the predictions for one plant.
plot(fit.spline, plotIds = "c10r29", plotType =  "derivatives")
plot(fit.spline, plotIds = "c10r29", plotType =  "derivatives2")

}
\seealso{
Other functions for fitting splines: 
\code{\link{fitSpline}()}
}
\concept{functions for fitting splines}