plot.HTPSpline: Plot the results of a fitted spline.

In statgenHTP: High Throughput Phenotyping (HTP) Data Analysis

Plot the results of a fitted spline.

Description

Plot the results of a fitted spline.

Usage

## S3 method for class 'HTPSpline'
plot(
  x,
  ...,
  plotType = c("predictions", "derivatives", "derivatives2"),
  genotypes = NULL,
  plotIds = NULL,
  title = NULL,
  output = TRUE,
  outFile = NULL,
  outFileOpts = NULL
)

Arguments

x	An object of class HTPSpline.
...	Ignored.
plotType	A character string indicating which spline component should be plotted, either predictions, derivatives or second derivatives ("derivatives2").
genotypes	A character vector indicating the genotypes for which spline components should be plotted.
plotIds	A character vector indicating the plotIds for which spline components should be plotted.
title	A character string used as title for the plot. If NULL a default title is added to the plot depending on plotType.
output	Should the plot be output to the current device? If FALSE only a (list of) ggplot object(s) is invisibly returned. Ignored if outFile is specified.
outFile	A character string indicating the .pdf file to which the plots should be written. If NULL, no file is written.
outFileOpts	A named list of extra options for the pdf outfile, e.g. width and height. See pdf for all possible options.

Value

A list of object of class ggplot is invisibly returned.

See Also

Other functions for fitting splines: fitSpline()

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")

statgenHTP documentation built on April 14, 2023, 9:12 a.m.