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Generic plot function for drFitFLModel objects.

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

Generic plot function for drFitFLModel objects.

Usage

# S3 method for drFitFLModel
plot(
  x,
  ec50line = TRUE,
  broken = TRUE,
  bp,
  n.xbreaks,
  n.ybreaks,
  log = c("xy"),
  pch = 1,
  colSpline = 1,
  colData = 1,
  cex.point = 1,
  cex.lab = 1.5,
  cex.axis = 1.3,
  y.lim = NULL,
  x.lim = NULL,
  lwd = 2,
  plot = TRUE,
  export = FALSE,
  height = 7,
  width = 9,
  out.dir = NULL,
  ...
)

Arguments

x

Object of class drFitFLModel, created with fl.drFitModel.

ec50line

(Logical) Show pointed horizontal and vertical lines at the EC50 value (TRUE) or not (FALSE).

broken

(Logical) If TRUE the x axis is broken provided this axis is logarithmic (using functionality in the CRAN package 'plotrix').

bp

(Numeric) Specifying the break point below which the dose is zero (the amount of stretching on the dose axis above zero in order to create the visual illusion of a logarithmic scale including 0). The default is the base-10 value corresponding to the rounded value of the minimum of the log10 values of all positive dose values. This argument is only working for logarithmic dose axes.

n.xbreaks

(Numeric) Number of breaks on the x-axis (if not log-transformed). The breaks are generated using pretty. Thus, the final number of breaks can deviate from the user input.

n.ybreaks

(Numeric) Number of breaks on the y-axis (if not log-transformed). The breaks are generated using pretty. Thus, the final number of breaks can deviate from the user input.#' @param pch (Numeric) Size of the raw data circles.

log

(Character) String which contains '"x"' if the x axis is to be logarithmic, '"y"' if the y axis is to be logarithmic and '"xy"' or '"yx"' if both axes are to be logarithmic. The default is "x". The empty string "" yields the original axes.

pch

(Numeric) Symbol used to plot data points.

colSpline

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

colData

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

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.

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).

lwd

(Numeric) Line width.

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 biosensor dose-response model fit.

Examples

# Create concentration values via a serial dilution
conc <- c(0, rev(unlist(lapply(1:18, function(x) 10*(2/3)^x))),10)

# Simulate response values via biosensor equation
response <- biosensor.eq(conc, y.min = 110, y.max = 6000, K = 0.5, n = 2) +
            0.01*6000*rnorm(10)

# Perform fit
TestRun <- fl.drFitModel(conc, response, drID = "test", control = fl.control())
#> 
#> 
#> === Dose response curve estimation ================
#> --- EC 50 -----------------------------------------
#> --> test
#> sensitivity: 0.495 | yEC50: 3012 | fold change: 65.42 | leakiness: 90.7
#> 
#> 

print(summary(TestRun))
#>      yEC50    y.min    y.max       fc         K        n yEC50.orig    K.orig
#> 1 3011.616 90.68406 5932.547 65.41996 0.4949696 2.038867   3011.616 0.4949696
#>   test
#> 1   NA
plot(TestRun)