makeBraidReport {braidReports}R Documentation

Render a BRAID Report

Description

Produces a one page report depicting the results of a full BRAID analysis for a single combination.

Usage

makeBraidReport(analysis, compounds, levels, limits, control = list())

Arguments

analysis

An object of class braidAnalysis produced by the runBraidAnalysis() or basicBraidAnalysis() functions

compounds

A length-2 character vector containing the names of the two compounds tested in the combination

levels

Two levels at which the IAE should be evaluated

limits

Two values representing the maximal achievable concentrations for the compounds tested, used to esitmate the IAE

control

A named list of additional control parameters adjusting the appearance of the resulting report

Details

This function attempts, however foolhardily, to encompass many of the details, plots, and values that the user might wish to report for a complete BRAID analysis of a given drug combination. All reports are built for a single 8.5-by-11 inch page, either in landscape or potrait orientation, but reports can be customized to contain more or less information. Here is a full list of what can appear in the BRAID report:

So the resulting report page can contain from six (simple layout) to twelve (dense layout) elements depicting different aspects of the BRAID analysis.

The precise appearance of the report page is controlled by various elements of the control parameter. Though the default value of the parameter is an empty list, several fields will be filled in if they are unspecified. The full set of possible control options is:

Value

A graphical object containing all plots and tables, arranged according to the desired format. The resulting object is optimized for a single page, either portrait or landscape as specified in control

Examples

surface <- synergisticExample
analysis <- runBraidAnalysis(measure~concA+concB, surface,
                             defaults=c(0,1), getCIs=FALSE)

report <- makeBraidReport(analysis,c("A Drug","B Drug"),
                          levels=c(0.5, 0.9),limits=c(5,5))
print(report)

control <- list(abbs=c("A","B"),units=c("\u00B5M"),leveltext=c("50","90"),
                xscale=scale_x_log10(breaks=c(0.1,0.5,2,10),
                labels=as.character),
                fillscale=scale_fill_viridis_c(option="A"),
                colorscale=scale_color_brewer(palette="Set1"),
                title="Example Analysis")
nextReport <- makeBraidReport(analysis,c("A Drug","B Drug"),
                              levels=c(0.5, 0.9),limits=c(5,5),
                              control=control)
print(nextReport)

[Package braidReports version 1.0.1 Index]