geom_braid_smooth: Smoothed BRAID Surfaces

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

Smoothed BRAID Surfaces

Description

Summarize and plot measurements of two inputs as a smoothed response surface

Usage

geom_braid_smooth(
  mapping = NULL,
  data = NULL,
  stat = "braid_smooth",
  position = "identity",
  ...,
  space = 1.5,
  trim = TRUE,
  shared = FALSE,
  npoints = 50,
  tight = FALSE,
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = TRUE
)

stat_braid_smooth(
  mapping = NULL,
  data = NULL,
  geom = "tile",
  position = "identity",
  ...,
  space = 1.5,
  trim = TRUE,
  shared = FALSE,
  npoints = 50,
  tight = 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.
...	Additional parameters to be passed to ggplot2::geom_tile()
space	Parameter specifying the separation between marginal tiles and the main grid. Describes the distance from the center of the marginal tile to the center of the nearest main grid tile, divided by the width or height of the tile. If a single value is provided, it is used for both left-right and top-bottom margin tiles. If two values are provided, the first is used for left-right margin tiles and the second is used for top-bottom margin tiles.
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.
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.
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

Like geom_braid, this function involves several pre-processing steps to allow quick visualization of drug combination data. These steps include summarizing duplicated measurements and offsetting non-finite plotted coordinates. In addition to these steps, geom_braid_smooth generates a regular, densely sampled grid of coordinates and smoothly interpolates the given data to produces a smoothed raster heatmap. Smoothing in the x- and y- directions is governed by the width and height aesthetic respectively; if these aesthetics are not included, they are estimated from the minimum spacing of the data.

Examples

surface <- synergisticExample

ggplot(surface,aes(x=concA,y=concB))+
   geom_braid_smooth(aes(fill=measure))+
    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.