plot.gcBootSpline: Generic plot function for 'gcBootSpline' objects.

In QurvE: Robust and User-Friendly Analysis of Growth and Fluorescence Curves

Generic plot function for gcBootSpline objects.

Description

Generic plot function for gcBootSpline objects.

Usage

## S3 method for class 'gcBootSpline'
plot(
  x,
  pch = 1,
  colData = 1,
  deriv = TRUE,
  colSpline = "dodgerblue3",
  cex.point = 1,
  cex.lab = 1.5,
  cex.axis = 1.3,
  lwd = 2,
  y.lim = NULL,
  x.lim = NULL,
  y.lim.deriv = NULL,
  plot = TRUE,
  export = FALSE,
  height = 7,
  width = 9,
  out.dir = NULL,
  combine = FALSE,
  ...
)

Arguments

x	object of class gcBootSpline, created with growth.gcBootSpline.
pch	(Numeric) Symbol used to plot data points.
colData	(Numeric or character) Contour color of the raw data circles.
deriv	(Logical) Show the derivatives (i.e., slope) over time in a secondary plot (TRUE) or not (FALSE).
colSpline	(Numeric or character) Spline line colour.
cex.point	(Numeric) Size of the raw data points.
cex.lab	(Numeric) Font size of axis titles.
cex.axis	(Numeric) Font size of axis annotations.
lwd	(Numeric) Spline line width.
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.
x.lim	(Numeric vector with two elements) Optional: Provide the lower (l) and upper (u) bounds on the x-axis of both growth curve and derivative plots 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.deriv	(Numeric vector with two elements) Optional: Provide the lower (l) and upper (u) bounds on the y-axis of the derivative 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.
plot	(Logical) Show the generated plot in the Plots pane (TRUE) or not (FALSE).
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.
combine	(Logical) Indicate whether both growth curves and parameter plots shall be shown within the same window.
...	Further arguments to refine the generated base R plot.

Value

A single plot with the all spline growth fits from the bootstrapping operation and statistical distribution of growth parameters if combine = TRUE or separate plots for growth fits and parameter distributions (if combine = FALSE).

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

# Introduce some noise into the measurements
data <- data + stats::runif(97, -0.01, 0.09)

# Perform bootstrapping spline fit
TestFit <- growth.gcBootSpline(time, data, gcID = "TestFit",
              control = growth.control(fit.opt = "s", nboot.gc = 50))

plot(TestFit, combine = TRUE, lwd = 0.5)

QurvE documentation built on May 29, 2024, 3 a.m.