geom_braid_contour: Smoothed BRAID Surface Contours

In braidReports: Visualize Combined Action Response Surfaces and Report BRAID Analyses

Smoothed BRAID Surface Contours

Description

Generate contours of a smoothed two-dimensional response surface

Usage

geom_braid_contour(
  mapping = NULL,
  data = NULL,
  stat = "braid_contour",
  position = "identity",
  ...,
  bins = NULL,
  binwidth = NULL,
  breaks = NULL,
  npoints = 50,
  tight = FALSE,
  trim = TRUE,
  shared = FALSE,
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = TRUE
)

stat_braid_contour(
  mapping = NULL,
  data = NULL,
  geom = "contour",
  position = "identity",
  ...,
  bins = NULL,
  binwidth = NULL,
  breaks = NULL,
  npoints = 50,
  tight = FALSE,
  trim = TRUE,
  shared = FALSE,
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = TRUE
)

Arguments

mapping	Set of aesthetic mappings created by aes(). If specified and inherit.aes = TRUE (the default), it is combined with the default mapping at the top level of the plot. You must supply mapping if there is no plot mapping.
data	The data to be displayed in this layer. There are three options: If NULL, the default, the data is inherited from the plot data as specified in the call to ggplot(). A data.frame, or other object, will override the plot data. All objects will be fortified to produce a data frame. See fortify() for which variables will be created. A function will be called with a single argument, the plot data. The return value must be a data.frame, and will be used as the layer data. A function can be created from a formula (e.g. ~ head(.x, 10)).
stat	The statistical transformation to use on the data for this layer. When using a ⁠geom_*()⁠ function to construct a layer, the stat argument can be used the override the default coupling between geoms and stats. The stat argument accepts the following: A Stat ggproto subclass, for example StatCount. A string naming the stat. To give the stat as a string, strip the function name of the stat_ prefix. For example, to use stat_count(), give the stat as "count". For more information and other ways to specify the stat, see the layer stat documentation.
position	A position adjustment to use on the data for this layer. This can be used in various ways, including to prevent overplotting and improving the display. The position argument accepts the following: The result of calling a position function, such as position_jitter(). This method allows for passing extra arguments to the position. A string naming the position adjustment. To give the position as a string, strip the function name of the position_ prefix. For example, to use position_jitter(), give the position as "jitter". For more information and other ways to specify the position, see the layer position documentation.
...	Other arguments passed on to layer()'s params argument. These arguments broadly fall into one of 4 categories below. Notably, further arguments to the position argument, or aesthetics that are required can not be passed through .... Unknown arguments that are not part of the 4 categories below are ignored. Static aesthetics that are not mapped to a scale, but are at a fixed value and apply to the layer as a whole. For example, colour = "red" or linewidth = 3. The geom's documentation has an Aesthetics section that lists the available options. The 'required' aesthetics cannot be passed on to the params. Please note that while passing unmapped aesthetics as vectors is technically possible, the order and required length is not guaranteed to be parallel to the input data. When constructing a layer using a ⁠stat_*()⁠ function, the ... argument can be used to pass on parameters to the geom part of the layer. An example of this is stat_density(geom = "area", outline.type = "both"). The geom's documentation lists which parameters it can accept. Inversely, when constructing a layer using a ⁠geom_*()⁠ function, the ... argument can be used to pass on parameters to the stat part of the layer. An example of this is geom_area(stat = "density", adjust = 0.5). The stat's documentation lists which parameters it can accept. The key_glyph argument of layer() may also be passed on through .... This can be one of the functions described as key glyphs, to change the display of the layer in the legend.
bins	Number of contour bins. Overridden by breaks.
binwidth	The width of the contour bins. Overridden by bins.
breaks	One of: Numeric vector to set the contour breaks A function that takes the range of the data and binwidth as input and returns breaks as output. A function can be created from a formula (e.g. ~ fullseq(.x, .y)). Overrides binwidth and bins. By default, this is a vector of length ten with pretty() breaks.
npoints	The number of interpolated values in the x- and y- directions that are used to generate the smoothed raster function
tight	If true, the generated raster will span the precise range of transformed and plotted data; this will produce a range of tiles that are strictly smaller than those produced by geom_braid (as those tiles extend above and below the plotted tile centers). If FALSE (the default), the interpolated values will be selected to span the same (slightly larger) range of values that would be covered by running geom_braid with the same parameters.
trim	Should values that are finite in one dimension be dropped if their finite coordinates lie outside the bounds of the main grid?
shared	Should marginal offsets and trimming be calculated separately for each facet if plots are faceted. If FALSE, the default, each facet will have its own bounds and marginal offsets; if TRUE, offsets will be calculated for the full data and shared across all facets.
na.rm	If FALSE, the default, missing values are removed with a warning. If TRUE, missing values are silently removed.
show.legend	logical. Should this layer be included in the legends? NA, the default, includes if any aesthetics are mapped. FALSE never includes, and TRUE always includes. It can also be a named logical vector to finely select the aesthetics to display.
inherit.aes	If FALSE, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions that define both data and aesthetics and shouldn't inherit behaviour from the default plot specification, e.g. borders().
geom	The geometric object to use to display the data for this layer. When using a ⁠stat_*()⁠ function to construct a layer, the geom argument can be used to override the default coupling between stats and geoms. The geom argument accepts the following: A Geom ggproto subclass, for example GeomPoint. A string naming the geom. To give the geom as a string, strip the function name of the geom_ prefix. For example, to use geom_point(), give the geom as "point". For more information and other ways to specify the geom, see the layer geom documentation.

Details

When evaluating a plotted response surface it is often more effective to plot the precise contours at which a set of levels is reached by the combination. Because ggplot2::stat_contour requires that data lie in an evenly space raster grid (and does not support duplicated values), it is difficult to apply to more discrete or irregularly sampled data. This function uses the same smoothing and interpolation utilities as geom_braid_smooth to preprocess and smooth data, which is then passed to the contour estimation code of ggplot2::stat_contour, producing contours which are smoothed and sufficiently regularly spaced.

Examples

surface <- antagonisticExample

ggplot(surface,aes(x=concA,y=concB))+
   geom_braid_smooth(aes(fill=measure))+
   geom_braid_contour(aes(z=measure),colour="black",breaks=((1:9)/10))+
    scale_x_log10("Drug A")+
    scale_y_log10("Drug B")+
    scale_fill_distiller("Effect",palette="RdYlBu")+
    coord_equal()

braidReports documentation built on Sept. 30, 2024, 1:06 a.m.