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Generic plot function for gcFitModel objects.

Source: R/growth_plots.R
plot.gcFitModel.Rd

Plot the results of a parametric model fit on growth vs. time data

Usage

# S3 method for gcFitModel
plot(
  x,
  raw = TRUE,
  pch = 1,
  colData = 1,
  equation = TRUE,
  eq.size = 1,
  colModel = "forestgreen",
  basesize = 16,
  cex.point = 2,
  lwd = 0.7,
  x.lim = NULL,
  y.lim = NULL,
  n.ybreaks = 6,
  plot = TRUE,
  export = FALSE,
  height = 6,
  width = 8,
  out.dir = NULL,
  ...
)

Arguments

x

A gcFittedModel object created with growth.gcFitModel or stored within a grofit or gcFit object created with growth.workflow or growth.gcFit, respectively.

raw

(Logical) Show the raw data within the plot (TRUE) or not (FALSE).

pch

(Numeric) Symbol used to plot data points.

colData

(Numeric or Character) Color used to plot the raw data.

equation

(Logical) Show the equation of the fitted model within the plot (TRUE) or not (FALSE).

eq.size

(Numeric) Provide a value to scale the size of the displayed equation.

colModel

(Numeric or Character) Color used to plot the fitted model.

basesize

(Numeric) Base font size.

cex.point

(Numeric) Size of the raw data points.

lwd

(Numeric) Spline line width.

x.lim

(Numeric vector with two elements) Optional: Provide the lower (l) and upper (u) bounds on the x-axis as a vector in the form c(l, u). If only the lower or upper bound should be fixed, provide c(l, NA) or c(NA, u), respectively.

y.lim

(Numeric vector with two elements) Optional: Provide the lower (l) and upper (u) bounds on y-axis of the growth curve plot as a vector in the form c(l, u). If only the lower or upper bound should be fixed, provide c(l, NA) or c(NA, u), respectively.

n.ybreaks

(Numeric) Number of breaks on the y-axis. The breaks are generated using scales::pretty_breaks. Thus, the final number of breaks can deviate from the user input.

plot

(Logical) Show the generated plot in the Plots pane (TRUE) or not (FALSE). If FALSE, a ggplot object is returned.

export

(Logical) Export the generated plot as PDF and PNG files (TRUE) or not (FALSE).

height

(Numeric) Height of the exported image in inches.

width

(Numeric) Width of the exported image in inches.

out.dir

(Character) Name or path to a folder in which the exported files are stored. If NULL, a "Plots" folder is created in the current working directory to store the files in.

...

Further arguments to refine the generated ggplot2 plot.

Value

A plot with the parametric fit.

Examples

# Create random growth dataset
rnd.dataset <- rdm.data(d = 35, mu = 0.8, A = 5, label = "Test1")

# Extract time and growth data for single sample
time <- rnd.dataset$time[1,]
data <- rnd.dataset$data[1,-(1:3)] # Remove identifier columns

# Perform parametric fit
TestFit <- growth.gcFitModel(time, data, gcID = "TestFit",
                 control = growth.control(fit.opt = "m"))
#> --> Try to fit model logistic
#> ....... OK
#> --> Try to fit model richards
#> ....... OK
#> --> Try to fit model gompertz
#> ....... OK
#> --> Try to fit model gompertz.exp
#> ... ERROR in nls(). For further information see help(growth.gcFitModel)
#> --> Try to fit model huang
#> .......... OK
#> --> Try to fit model baranyi
#> ........ OK
#> 
#> Best fitting model: ~baranyi

plot(TestFit, basesize = 18, eq.size = 1.5)
#> Scale for y is already present.
#> Adding another scale for y, which will replace the existing scale.
#> Scale for colour is already present.
#> Adding another scale for colour, which will replace the existing scale.