plotResponseSurface {BIGL}  R Documentation 
Plot the 3dimensional response surface predicted by one of the null
models. This plot allows for a visual comparison between the null
model prediction and observed points. This function is mainly used
as the workhorse of plot.ResponseSurface
method.
plotResponseSurface(
data,
fitResult = NULL,
transforms = fitResult$transforms,
predSurface = NULL,
null_model = c("loewe", "hsa", "bliss", "loewe2"),
colorPalette = c("blue", "grey70", "red"),
colorBy = "none",
colorPoints = c("black", "sandybrown", "brown", "white"),
breaks = c(Inf, 0, Inf),
radius = NULL,
logScale = TRUE,
colorfun = median,
zTransform = function(x) x,
add = FALSE,
main = "",
legend = TRUE,
xat = "actual",
yat = "actual",
plotfun = NULL,
...
)
data 
Doseresponse dataframe. 
fitResult 
Monotherapy (onaxis) model fit, e.g. produced by

transforms 
Transformation functions. If nonnull, 
predSurface 
Vector of all predicted responses based on

null_model 
If 
colorPalette 
Vector of color names for surface 
colorBy 
This parameter determines values on which coloring is based
for the 3dimensional surface. If matrix or a data frame with 
colorPoints 
Colors for offaxis and onaxis points. Character vector of length four with colors for 1) offaxis points; 2) onaxis points of the first drug (i.e. second drug is dosed at zero); 3) onaxis points of the second drug; 4) onaxis points where both drugs are dosed at zero. 
breaks 
Numeric vector with numerical breaks. To be used in conjunction
with 
radius 
Radius of spheres. If missing, an educated guess based on number of digits in average effect will be made. 
logScale 
Draw doses on logscale (setting zeroes to be finite constant) 
colorfun 
If replicates in 
zTransform 
Optional transformation function for zaxis. By default, identity function is used. 
add 
Add the predicted response surface to an existing plot. Will not
draw any points, just the surface. Must be called after another call to

main 
Fixed nonmoving title for the 3D plot 
legend 
Whether legend should be added 
xat 
xaxis ticks: "pretty", "actual" or a numeric vector 
yat 
yaxis ticks: "pretty", "actual" or a numeric vector 
plotfun 
If replicates for dose combinations in 
... 
Further arguments to format axis labels 
Title for the plot and legend are drawn as bitmaps and do not rotate with the rest of the plot. Since they are bitmaps, they do not scale properly, hence resizing window will result in unappealing visuals. For them to look properly, it suffices to set the appropriate RGL window size and rerun the plotting command.
Plot is shown on a rgl device.
## Not run:
data < subset(directAntivirals, experiment == 1)
## Data must contain d1, d2 and effect columns
fitResult < fitMarginals(data)
data_mean < aggregate(effect ~ d1 + d2, data = data[, c("d1", "d2", "effect")],
FUN = mean)
## Construct the surface from marginal fit estimates based on HSA
## model and color it by mean effect level
plotResponseSurface(data, fitResult, null_model = "hsa",
colorBy = data_mean, breaks = 10^(c(0, 3, 4, 6)),
colorPalette = c("grey", "blue", "green"))
## Response surface based on Loewe additivity model and colored with
## rainbow colors. Legend will not be displayed in any case.
plotResponseSurface(data, fitResult, null_model = "loewe",
colorBy = "colors", colorPalette = rainbow(6))
## End(Not run)