formatResponseMap: Format Response and Error Maps

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

Description

Format response maps as activity maps using a multicolor gradient or error maps using a bidirectional gradient.

Usage

formatResponseMap(rmap, palette = NULL, cscale = NULL, xl = expression(Conc[A]),
					yl = expression(Conc[B]), zl = "Activity")
formatDifferenceMap(rmap, zcenter = NULL, xl = expression(Conc[A]),
					yl = expression(Conc[B]), zl = "Diff")

Arguments

rmap	a ggplot2 plot object depicting a response map, produced by the function responseMap
palette	a character vector or two or more colors defining the colorscale to be applied to the fill variable in the plot.
cscale	a value around which the colorscale applied to the fill variable will be centered. If NULL (the default), the colorscale will range from the minimum fill variable to the maximum.
xl	The character string or expression used to label the x-axis
yl	The character string or expression used to label the y-axis
zl	The character string or expression used to label the colorscale representing the response variable
zcenter	the value that forms the centerpoint (white) in the bidirectional color scale. If NULL (the default), the default setting for scale_fill_gradient2 is used.

Details

These functions are largely convenience functions, taking a response map produced by responseMap and formatting it with colorscales and axis labels. formatResponseMap with a multicolor gradient; by default it uses a modified 'jet' colormap, ranging from dark red to dark green, rather than the traditional dark blue. We find this function useful for visualizing response surfaces representing variables such as cytotoxicity, cell viability, enzyme activity, etc. The other formats the response map with a bidirectional color gradient (using the ggplot2 function scale_fill_gradient2; we find this format ideal for visualizing error maps.

Value

A ggplot2 plot object, with the appropriate scales and labels added.

Author(s)

Nathaniel R. Twarog

References

Twarog, N.R., Stewart, E., Vowell Hamill, C., and Shelat, A. BRAID: A Unifying Paradigm for the Analysis of Combined Drug Action. Scientific Reports In Press (2016).

See Also

responseMap

Examples

data(es8olatmz,package="braidrm")
rmap <- responseMap(act~conc1+conc2,es8olatmz)
formatResponseMap(rmap,xl="Olaparib",yl="TMZ",zl="Survival")
formatDifferenceMap(rmap,zcenter=-1)

nathanieltwarog/braidReports documentation built on May 23, 2019, 12:19 p.m.