R: Plot function for class psHDM

plot.psHDM {statgenHTP}

R Documentation

Plot function for class psHDM

Description

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

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")