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Generic plot function for drFitModel objects.

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

Generic plot function for drFitModel objects.

Usage

# S3 method for drFitModel
plot(
  x,
  type = c("confidence", "all", "bars", "none", "obs", "average"),
  ec50line = TRUE,
  add = FALSE,
  broken = TRUE,
  bp,
  gridsize = 200,
  log = "x",
  n.xbreaks,
  n.ybreaks,
  x.lim,
  y.lim,
  pch = 1,
  cex.point,
  cex.axis = 1,
  cex.lab = 1.3,
  col = 1,
  lwd = 2,
  lty = 2,
  xlab,
  ylab,
  legend = TRUE,
  legendText,
  legendPos,
  cex.legend = NULL,
  plot = TRUE,
  export = FALSE,
  height = 7,
  width = 9,
  out.dir = NULL,
  ...
)

Arguments

x

object of class drFitModel, created with growth.drFitModel.

type

(Character) Specify how to plot the data. There are currently 5 options: "average" (averages and fitted curve(s); default), "none" (only the fitted curve(s)), "obs" (only the data points), "all" (all data points and fitted curve(s)), "bars" (averages and fitted curve(s) with model-based standard errors (see Details)), and "confidence" (confidence bands for fitted curve(s)).

ec50line

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

add

(Logical) If TRUE then add to already existing plot.

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.

gridsize

(Numeric) Number of points in the grid used for plotting the fitted curves.

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.

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.

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

(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.

pch

(Numeric) Symbol used to plot data points.

cex.point

(Numeric) Size of the raw data points.

cex.axis

(Numeric) Font size of axis annotations.

cex.lab

(Numeric) Font size of axis titles.

col

(Logical or a vector of colors) If TRUE default colours are used. If FALSE (default) no colors are used.

lwd

(Numeric) Line width.

lty

(Numeric) Specify the line type.

xlab

(Character) An optional label for the x axis.

ylab

(Character) An optional label for the y axis.

legend

(Logical) If TRUE a legend is displayed.

legendText

(Character) Specify the legend text (the position of the upper right corner of the legend box).

legendPos

(Numeric) Vector of length 2 giving the position of the legend.

cex.legend

numeric specifying the legend text size.

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.

...

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

Value

A plot with the dose-response model fit.

References

Christian Ritz, Florent Baty, Jens C. Streibig, Daniel Gerhard (2015). Dose-Response Analysis Using R. PLoS ONE 10(12): e0146021. DOI: 10.1371/journal.pone.0146021

Examples

conc <- c(0, rev(unlist(lapply(1:18, function(x) 10*(2/3)^x))),10)
response <- c(1/(1+exp(-0.7*(4-conc[-20])))+stats::rnorm(19)/50, 0)

TestRun <- growth.drFitModel(conc, response, drID = "test")

print(summary(TestRun))
#>        EC50.Estimate EC50.Std..Error EC50.Lower EC50.Upper     yEC50      test
#> e:1:50      4.189491      0.06802249   4.045976   4.333006 0.4655031 mu.linfit
#>        model
#> e:1:50  W1.3
plot(TestRun)