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Plot function for class psHDM

Source: R/plot.psHDM.R
plot.psHDM.Rd

This plot function provides five plots for objects of the class psHDM after fitting (fitSplineHDM) or predicting (predict.psHDM): (1) Population-specific growth curves (popTra), (2) Population and genotype-specific growth curves (for all genotypes, popGenoTra), (3) First-order derivative of the population and genotype-specific growth curves (for all genotypes, popGenoDeriv), (4) Genotype-specific deviations (for all genotypes, genoDev), and (5) Genotype- and plot-specific growth curves (for a selection of genotypes, genoPlotTra). If standard errors are available, 95% point wise confidence intervals are depicted.

Usage

# S3 method for class 'psHDM'
plot(
  x,
  ...,
  plotType = c("popTra", "popGenoTra", "popGenoDeriv", "genoDev", "genoPlotTra"),
  genotypes = NULL,
  genotypeNames = NULL,
  genotypeOrder = NULL,
  xlab = "Time",
  ylab = expression(tilde(y)[pgi](t)),
  title = NULL,
  themeSizeHDM = 15,
  output = TRUE,
  outFile = NULL,
  outFileOpts = NULL
)

Arguments

x

An object of class "psHDM" as obtained after fitting (fitSplineHDM) or predicting (predict.psHDM),

...

Not used.

plotType

A character string indicating which plot should be made.

genotypes

A character vector with the genotypes for which plots at plot level are desired. Only used when plotType == "genoPlotTra".

genotypeNames

A character vector with alternative names for the plotted genotypes (genotypes). If NULL the names of the genotypes are used. Only used when plotType == "genoPlotTra".

genotypeOrder

A vector with the order of the selected genotypes (genotypes). If NULL then the order in the data is preserved. Only used when plotType == "genoPlotTra".

xlab

The x-axis label of the plot.

ylab

The y-axis label of the plot.

title

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

themeSizeHDM

Reference size for the theme

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.

References

Pérez-Valencia, D.M., Rodríguez-Álvarez, M.X., Boer, M.P. et al. A two-stage approach for the spatio-temporal analysis of high-throughput phenotyping data. Sci Rep 12, 3177 (2022). doi:10.1038/s41598-022-06935-9

See also

Other functions for fitting hierarchical curve data models: fitSplineHDM(), predict.psHDM()

Examples

## The data from the Phenovator platform have been corrected for spatial
## trends and outliers for single observations have been removed.

## We need to specify the genotype-by-treatment interaction.
## Treatment: water regime (WW, WD).
spatCorrectedArch[["treat"]] <- substr(spatCorrectedArch[["geno.decomp"]],
                                      start = 1, stop = 2)
spatCorrectedArch[["genoTreat"]] <-
  interaction(spatCorrectedArch[["genotype"]],
             spatCorrectedArch[["treat"]], sep = "_")

## Fit P-Splines Hierarchical Curve Data Model for selection of genotypes.
fit.psHDM  <- fitSplineHDM(inDat = spatCorrectedArch,
                          trait = "LeafArea_corr",
                          genotypes = c("GenoA14_WD", "GenoA51_WD",
                                       "GenoB11_WW", "GenoB02_WD",
                                       "GenoB02_WW"),
                          time = "timeNumber",
                          pop = "geno.decomp",
                          genotype = "genoTreat",
                          plotId = "plotId",
                          difVar = list(geno = FALSE, plot = FALSE),
                          smoothPop = list(nseg = 4, bdeg = 3, pord = 2),
                          smoothGeno = list(nseg = 4, bdeg = 3, pord = 2),
                          smoothPlot = list(nseg = 4, bdeg = 3, pord = 2),
                          weights = "wt",
                          trace = FALSE)

## Plot the P-Spline predictions at the three levels of the hierarchy

## Population-specific growth curves.
plot(fit.psHDM,
    plotType = "popTra")


## Population and genotype-specific growth curves.
plot(fit.psHDM,
    plotType = "popGenoTra")


## First-order derivative of the population- and genotype-specific growth curves.
plot(fit.psHDM,
    plotType = "popGenoDeriv")


## Genotype-specific deviations.
plot(fit.psHDM,
    plotType = "genoDev")


## Genotype- and plot-specific growth curves.
plot(fit.psHDM,
    plotType = "genoPlotTra")