qplotDrc: Plotting fitted dose-response curves using ggplot2

In DoseResponse/bmd: Benchmark dose estimation for dose-response data

Plotting fitted dose-response curves using ggplot2

Description

qplotDrc displays fitted curves and observations in the same plot window, distinguishing between curves by different plot symbols and line types or colours using ggplot2.

Usage

  
  qplotDrc(x, add = FALSE, level = NULL, type = c("average", "all", "bars", "none", "obs", "confidence"), 
            gridsize = 100, xtrans = "pseudo_log", xlab, xlim, 
            ytrans = NULL, ylab, ylim, col = FALSE,
            normal = FALSE, normRef = 1, confidence.level = 0.95)

Arguments

x	an object of class 'drc'.
add	logical. If TRUE then the functions returns a list of plot layers to be added to an already existing ggplot.
level	vector of curve levels to plot. To plot only the curves specified by their names.
type	a character string specifying 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)).
gridsize	numeric. Number of points in the grid used for plotting the fitted curves.
xtrans	Transformation to use on the x-axis. The default is "pesudo_log", which is a logarithmic transformation with a smooth transition to 0. Other options include (among others) "log" and "identity". Can be overridden by adding a scale using the scale_x_continuous function.
xlab	an optional label for the x axis.
xlim	a numeric vector of length two, containing the lower and upper limit for the x axis.
ytrans	Transformation to use on the y-axis. The default is no transformation. Other options include (among others) "pseudo_log" and "log" and. Can be overridden by adding a scale using the scale_y_continuous function.
ylab	an optional label for the y axis.
ylim	a numeric vector of length two, containing the lower and upper limit for the y axis.
col	logical. If TRUE default ggplot colours are used, can be overridden by scale_color_manual. If FALSE (default) no colours are used.
normal	logical. If TRUE the plot of the normalized data and fitted curves are shown (for details see Weimer et al. (2012) for details).
normRef	numeric specifying the reference for the normalization (default is 1).
confidence.level	confidence level for error bars and confidence bands. Defaults to 0.95.

Details

This function largely seeks to mimic the behaviour of the plot method for the drc package using the ggplot2 package for plotting.

The use of xlim allows changing the range of the x axis, extrapolating the fitted dose-response curves. Note that changing the range on the x axis may also entail a change of the range on the y axis.

See colors for the available colours.

Suitable labels are automatically provided.

The model-based standard errors used for the error bars are calculated as the fitted value plus/minus the estimated error times the 1-(alpha/2) quantile in the t distribution with degrees of freedom equal to the residual degrees of freedom for the model (or using a standard normal distribution in case of binomial and poisson data), where alpha=1-confidence.level. The standard errors are obtained using the predict method with the arguments interval = "confidence" and level=confidence.level.

Value

A ggplot object. If the option add is used, a list of ggplot layers is returned.

Author(s)

Jens Riis Baalkilde. Based on plot.drc by Christian Ritz and Jens C. Streibig with Contributions from Xiaoyan Wang and Greg Warnes.

References

Weimer, M., Jiang, X., Ponta, O., Stanzel, S., Freyberger, A., Kopp-Schneider, A. (2012) The impact of data transformations on concentration-response modeling. Toxicology Letters, 213, 292–298.

Examples

## Fitting models to be plotted below
ryegrass.m1 <- drm(rootl~conc, data = ryegrass, fct = LL.4())
ryegrass.m2 <- drm(rootl~conc, data = ryegrass, fct = LL.3())  # lower limit fixed at 0

## Plotting observations and fitted curve for the first model
p <- qplotDrc(ryegrass.m1) 
p

## Add confidence region for the first model.
p + qplotDrc(ryegrass.m1, type="confidence", add = TRUE)$confBandLayer 

## Plot both models
p + qplotDrc(ryegrass.m2, add = TRUE)$curveLayer

## Fitting model to be plotted below
spinach.m1 <- drm(SLOPE~DOSE, CURVE, data = spinach, fct = LL.4())

## Plot with no colours
qplotDrc(spinach.m1)

## Plot with default colours
qplotDrc(spinach.m1, col = TRUE)

## Plot with specified colours
qplotDrc(spinach.m1, col = TRUE) + 
  scale_color_manual(values = c("darkolivegreen4", "lightcoral", "goldenrod","darkslategray4", "plum4"))

## Plot of curves 1 and 2 only
qplotDrc(spinach.m1, level = c(1,4))

## Plot with confidence regions
qplotDrc(spinach.m1, col = TRUE, type = "confidence")

## Plot points and add confidence regions. Confidence regions are coloured by the "fill" aesthetic.
## Customising the x scale by adding a new scale.
qplotDrc(spinach.m1, col = TRUE, type = "confidence") +
  qplotDrc(spinach.m1, col = TRUE, type = "average", add = TRUE)$obsLayer + 
  scale_color_manual(values = c("darkolivegreen4", "lightcoral", "goldenrod","darkslategray4", "plum4"))+ 
  scale_fill_manual(values = c("darkolivegreen4", "lightcoral", "goldenrod","darkslategray4", "plum4")) +
  scale_x_continuous(trans = scales:::pseudo_log_trans(sigma = 0.2, base = exp(1)))

DoseResponse/bmd documentation built on March 29, 2025, 4:36 p.m.