plot.gcFitLinear: Generic plot function for 'gcFittedLinear' objects. Plot the...

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

Generic plot function for gcFittedLinear objects. Plot the results of a linear regression on ln-transformed data

Description

plot.gcFitLinear shows the results of a linear regression on log-transformed data and visualizes raw data, data points included in the fit, the tangent obtained by linear regression, and the lag time.

Usage

## S3 method for class 'gcFitLinear'
plot(
  x,
  log = "y",
  which = c("fit", "diagnostics", "fit_diagnostics"),
  pch = 21,
  cex.point = 1,
  cex.lab = 1.5,
  cex.axis = 1.3,
  lwd = 2,
  color = "firebrick3",
  y.lim = NULL,
  x.lim = NULL,
  plot = TRUE,
  export = FALSE,
  height = ifelse(which == "fit", 7, 5),
  width = ifelse(which == "fit", 9, 9),
  out.dir = NULL,
  ...
)

Arguments

x	A gcFittedLinear object created with growth.gcFitLinear or stored within a grofit or gcFit object created with growth.workflow or growth.gcFit, respectively.
log	("x" or "y") Display the x- or y-axis on a logarithmic scale.
which	("fit" or "diagnostics") Display either the results of the linear fit on the raw data or statistical evaluation of the linear regression.
pch	(Numeric) Shape of the raw data symbols.
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) Line width.
color	(Character string) Enter color either by name (e.g., red, blue, coral3) or via their hexadecimal code (e.g., #AE4371, #CCFF00FF, #0066FFFF). A full list of colors available by name can be found at http://www.stat.columbia.edu/~tzheng/files/Rcolor.pdf
y.lim	(Numeric vector with two elements) Optional: Provide the lower (l) and upper (u) bounds on y-axis as a vector in the form c(l, u).
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).
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.
...	Further arguments to refine the generated base R plot.

Value

A plot with the linear 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 linear fit
TestFit <- growth.gcFitLinear(time, data, gcID = "TestFit",
                 control = growth.control(fit.opt = "l"))

plot(TestFit)

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