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Generic plot function for flBootSpline objects.

Source: R/fluorescence_plots.R
plot.flBootSpline.Rd

Generic plot function for flBootSpline objects.

Usage

# S3 method for flBootSpline
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 flBootSpline, created with flBootSpline.

pch

(Numeric) Size of the raw data circles.

colData

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

deriv

(Logical) Show the derivatives (i.e., slope) over time in a secondary plot (TRUE) or not (FALSE).

colSpline

(Numeric or Character) Color used to plot the splines.

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 fluorescence 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 fluorescence 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.

...

Additional arguments. This has currently no effect and is only meant to fulfill the requirements of a generic function.

Value

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

Examples

# load example dataset
input <- read_data(data.growth = system.file("lac_promoters.xlsx", package = "QurvE"),
                   data.fl = system.file("lac_promoters.xlsx", package = "QurvE"),
                   sheet.growth = 1,
                   sheet.fl = 2 )
#> Sample data are stored in columns. If they are stored in row format, please run read_data() with data.format = 'row'.

# Extract time and normalized fluorescence data for single sample
time <- input$time[4,]
data <- input$norm.fluorescence[4,-(1:3)] # Remove identifier columns

# Perform linear fit
TestFit <- flBootSpline(time = time,
                       fl_data = data,
                       ID = "TestFit",
                       control = fl.control(fit.opt = "s", x_type = "time",
                       nboot.fl = 50))

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