GRbox {GRmetrics} | R Documentation

## Boxplots of a given GR metric

### Description

Given a SummarizedExperiment object created by `GRfit`, this function creates boxplots according to the parameters below.

### Usage

    GRbox(fitData, metric, groupVariable, pointColor, factors = "all",
      wilA = NULL, wilB = NULL, plotly = TRUE)

### Arguments

`fitData` | a SummarizedExperiment object, generated by the GRfit function.
`metric` | the GR metric (GR50, GRinf, h_GR, GRmax, GEC50, or GR_AOC) or traditional metric (IC50, Einf, h, Emax, EC50, or AUC) that will be used for the boxplot.
`groupVariable` | the name of the variable from data (e.g. drug, cell-line, etc.) to select factors from.
`pointColor` | a variable that defines the coloring of the points overlayed on the boxplot.
`factors` | a vector of values of "groupVariable" of data that define which variables to make boxplots for. By default, a separate boxplot is made for each unique value of groupVariable.
`wilA` | one value or a vector of values from "factors", i.e. a subset of the boxplots. If specified, a one-sided Wilcoxon rank sum test (wilcox.test) will be performed between "wilA" and "wilB" and the results will be displayed on the figure. The null hypothesis that the values from "wilA" and "wilB" have the same mean will be tested against the alternative hypothesis that the mean of the "wilB" values is greater than that of the "wilA" values.
`wilB` | one value or a vector of values from "factors", i.e. a subset of the boxplots (not overlapping "wilA").
`plotly` | a logical value indicating whether to output a ggplot2 graph or an interactive ggplotly graph

### Details

Given a SummarizedExperiment object created by `GRfit`, this function creates boxplots of a given GR metric (GR50, GRmax, etc.) or traditional metric (IC50, Emax, etc.) for values of the grouping variable. The results can be viewed in a static ggplot image or an interactive plotly graph.

By default, a boxplot is created for all unique values of the grouping variable. The "factors" parameter can be used to specify a smaller subset of values for which to create boxplots. Points are overlayed on the boxplots and they can be colored by the variable specified in the pointColor parameter. If pointColor is set to NULL, the points will all be black. The results can be viewed in a static ggplot image or an interactive plotly graph.

### Value

ggplot2 or ggplotly boxplots of the factors along the x-axis, with points colored by the given variable.

### Author(s)

Nicholas Clark

### See Also

To create the object needed for this function, see `GRfit`. For other visualizations, see `GRdrawDRC` and `GRscatter`. For online GR calculator and browser, see http://www.grcalculator.org.

### Examples

    # Load Case A (example 1) input
    data("inputCaseA")
    head(inputCaseA)
    # Run GRfit function with case = "A"
    output1 = GRfit(inputData = inputCaseA,
    groupingVariables = c('cell_line','agent', 'perturbation','replicate',
    'time'))
    GRbox(output1, metric ='GRinf',
    groupVariable = 'cell_line', pointColor = 'agent' , factors = c('BT20',
    'MCF10A'))
    GRbox(output1, metric ='GRinf',
    groupVariable = 'cell_line', pointColor = 'cell_line' ,
    factors = c('BT20', 'MCF10A'), plotly = FALSE)
    GRbox(output1, metric = 'GR50', groupVariable = 'cell_line',
    pointColor = 'cell_line', wilA = "BT20", wilB = c("MCF7","MCF10A"))

[Package GRmetrics version 1.8.1 Index]