Plot function for class TP

Plotting function for objects of class TP. Plots the layout of the platform for different time points within the TP object. Also a boxplot can be made for selected traits and time points and a plot of correlations between time points. Finally the raw data can be displayed per genotype. A detailed description and optional extra parameters for the different plots are given in the sections below.

Usage

# S3 method for class 'TP'
plot(
  x,
  ...,
  plotType = c("layout", "box", "cor", "raw"),
  timePoints = names(x),
  title = NULL,
  traits = NULL,
  output = TRUE,
  outFile = NULL,
  outFileOpts = NULL
)

Arguments

x: An object of class TP.
...: Extra plot options. Described per plotType in their respective section.
plotType: A single character string indicating which plot should be made. See the sections below for a detailed explanation of the plots.
timePoints: A character or numeric vector indicating the time points to be plotted. When using a character string to reference a time point, the value has to be an exact match to one of the existing timePoints. When using a number it will be matched by its number ("timeNumber") in the timePoints attribute of the TP object.
title: A character string used as title for the plot. If NULL a default title is added to the plot depending on plotType.
traits: A character vector indicating the traits to be plotted. If plotType = "layout" only a single trait may be plotted. For the other plotTypes, providing multiple traits will create multiple plots.
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

Depending on the plot type, either a ggplot object or a list of ggplot objects is invisibly returned.

Layout Plot

Plots the layout of the platform for selected time points (all available time points by default). This plot can only be made for time points that contain both row (rowNum) and column (colNum) information. If either one of those is missing the timePoint is skipped with a warning. If replicates (repId) are available, a black line is plotted between diffent replicates. Missing plots are indicated in white. This can either be single plots in a time point or complete missing columns or rows.
Extra parameter options:

showGeno: Should individual genotypes be labeled in the plot? Defaults to FALSE
highlight: A character vector of genotypes to be highlighted in the plot.

Box Plot

Creates a boxplot per selected trait grouped by time point (all available time points by default). Extra parameter options:

groupBy: A character string indicating a column in TP by which the boxes in the plot should be grouped. By default the boxes are grouped per time point.
colorBy: A character string indicating a column in TP by which the boxes are colored. Coloring will be done within the groups indicated by the groupBy parameter, e.g. per replicate within each time point using repId.
orderBy: A character string indicating the way the boxes should be ordered. Either "alphabetic" for alphabetical ordering of the groups, "ascending" for ordering by ascending mean, or "descending" for ordering by descending mean. By default boxes are ordered alphabetically.

Correlation Plot

Draws a heatmap of correlations of raw data between time points per selected trait for selected time points (all available time points by default).

Raw data plot

Create a plot of the raw data of the selected trait over time for selected time points (all available time points by default). Plots are grouped by genotype, or by genotype x treatment when the geno.decomp option is specified. By default, all the genotypes will be plotted which might take time and memory when the output is not saved in a file (see parameter outFile). Extra parameter options:

genotypes: A character vector indicating the genotypes to be plotted.
geno.decomp: A character vector indicating the grouping of the genotypes to be plotted.
plotLine: Should the data be displayed as lines? Default is FALSE.

Examples

# \donttest{
## Create a TP object containing the data from the Phenovator.
phenoTP <- createTimePoints(dat = PhenovatorDat1,
                            experimentName = "Phenovator",
                            genotype = "Genotype",
                            timePoint = "timepoints",
                            repId = "Replicate",
                            plotId = "pos",
                            rowNum = "y", colNum = "x",
                            addCheck = TRUE,
                            checkGenotypes = c("check1", "check2",
                                               "check3", "check4"))
#> Warning: The following plotIds have observations for less than 50% of the time points:
#> c24r41, c7r18, c7r49

## Plot the layout for the third time point with the check genotypes
## highlighted
plot(phenoTP,
     plotType = "layout",
     timePoints = 3,
     highlight = c("check1", "check2", "check3", "check4"))


## Create a boxplot for "EffpsII" with 5 time points and boxes colored
## by "repId" within time point.
plot(phenoTP,
     plotType = "box",
     traits = "EffpsII",
     timePoints = 1:5,
     colorBy = "repId")


## Create a correlation plot for "EffpsII" for a selection of time points.
plot(phenoTP,
     plotType = "cor",
     traits = "EffpsII",
     timePoints = seq(from=1, to=73, by=5))


## Plot the raw data of four genotypes for the trait "EffpsII":
plot(phenoTP,
     traits = "EffpsII",
     plotType = "raw",
     genotypes = c("G001","G002","check1","check2"))

# }