plotResponseSurface: Plot response surface

In BIGL: Biochemically Intuitive Generalized Loewe Model

Plot response surface

Description

Plot the 3-dimensional 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.

Usage

plotResponseSurface(
  data,
  fitResult = NULL,
  transforms = fitResult$transforms,
  predSurface = NULL,
  null_model = c("loewe", "hsa", "bliss", "loewe2"),
  colorPalette = c("red", "grey70", "blue"),
  colorPaletteNA = "grey70",
  colorBy = "none",
  addPoints = TRUE,
  colorPoints = c("black", "sandybrown", "brown", "white"),
  breaks,
  radius = 4,
  logScale = TRUE,
  colorfun = median,
  zTransform = function(x) x,
  add = FALSE,
  main = "",
  legend = FALSE,
  xat = "actual",
  yat = "actual",
  plotfun = NULL,
  gradient = TRUE,
  width = 800,
  height = 800,
  title = "",
  digitsFunc = function(x) {
     x
 },
  ...
)

Arguments

data	Object "data" from the output of fitSurface
fitResult	Object "fitResult" from the output of fitSurface
transforms	Object "transforms" from the output of fitSurface
predSurface	Vector of all predicted responses based on expand.grid(uniqueDoses). If not supplied, it will be computed with predictOffAxis function.
null_model	If predSurface is not supplied, it is computed using one of the available null models, i.e. "loewe", "hsa", "bliss" and "loewe2". See also fitSurface.
colorPalette	Vector of color names for surface
colorPaletteNA	Color used in the matrix of colours when the combination of doses doesn't exist (NA)
colorBy	This parameter determines values on which coloring is based for the 3-dimensional surface. If matrix or a data frame with d1 and d2 columns is supplied, dose combinations from colorBy will be matched automatically to the appropriate dose combinations in data. Unmatched dose combinations will be set to 0. This is especially useful for plotting results for off-axis estimates only, e.g. off-axis Z-scores or maxR test statistics. If colorBy = "colors", surface will be colored using colors in colorPalette argument.
addPoints	Boolean whether the dose points should be included
colorPoints	Colors for off-axis and on-axis points. Character vector of length four with colors for 1) off-axis points; 2) on-axis points of the first drug (i.e. second drug is dosed at zero); 3) on-axis points of the second drug; 4) on-axis points where both drugs are dosed at zero.
breaks	Numeric vector with numerical breaks. To be used in conjunction with colorPalette argument. If named, the labels will be displayed in the legend
radius	Size of spheres (default is 4)
logScale	Draw doses on log-scale (setting zeroes to be finite constant)
colorfun	If replicates in colorBy variable are present, these will be aggregated using colorfun function. This can also be a custom function returning a scalar.
zTransform	Optional transformation function for z-axis. By default, identity function is used.
add	(deprecated) Add the predicted response surface to an existing plot. Will not draw any points, just the surface. Must be called after another call to plotResponseSurface.
main	Fixed non-moving title for the 3D plot
legend	Whether legend should be added (default FALSE)
xat	x-axis ticks: "pretty", "actual" or a numeric vector
yat	y-axis ticks: "pretty", "actual" or a numeric vector
plotfun	If replicates for dose combinations in data are available, points can be aggregated using plotfun function. Typically, it will be mean, median, min or max but a custom-defined function returning a scalar from a vector is also possible.
gradient	Boolean indicating whether colours should be interpolated between breaks (default TRUE). If FALSE, colorPalette must contain length(breaks)-1 colours
width	Width in pixels (optional, defaults to 800px).
height	Height in pixels (optional, defaults to 800px).
title	String title (default "")
digitsFunc	Function to be applied to the axis values
...	Further arguments to format axis labels

Value

Plotly plot

Examples

## 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.
  plotResponseSurface(data, fitResult, null_model = "loewe", breaks = c(-Inf, 0, Inf),
                      colorBy = "colors", colorPalette = rainbow(6))

## End(Not run)

BIGL documentation built on July 9, 2023, 7:15 p.m.