GRscatter: Scatterplot of a given GR metric
In uc-bd2k/GRmetrics_old: Calculate growth-rate inhibition (GR) metrics

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/GRscatter.R

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

1	GRscatter(fitData, metric, variable, xaxis, yaxis, plotly = TRUE)

`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 scatterplot.
`variable`	The name of the variable from data (e.g. drug, cell-line, etc.) to select factors from.
`xaxis`	a vector of values of "variable" of data to be used for the scatterplot's x-axis
`yaxis`	a vector of values of "variable" of data to be used for the scatterplot's y-axis
`plotly`	a logical value indicating whether to output a ggplot2 graph or a ggplotly graph

Given a SummarizedExperiment object created by GRfit, this function creates a scatterplot of a given GR metric (GR50, GRmax, etc.) or traditional metric (IC50, Emax, etc.) with the "xaxis" values plotted against the "yaxis" values. The results can be viewed in a static ggplot image or an interactive plotly graph.

The xaxis and yaxis vectors must be of the same length or at least one must be of length one. For each pair of values xaxis[i] and yaxis[i], the function will create a scatterplot (all on one graph) of the specified GR metric. If a vector is of length one, it will be repeated to the length of the other vector.

a ggplot2 or ggplotly scatterplot of the x-axis variable(s) versus the y-axis variable(s) for the given GR metric

Nicholas Clark

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

# 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'))
GRscatter(output1, 'GR50', 'agent', c('drugA','drugD'), 'drugB')
GRscatter(output1, 'GR50', 'agent', c('drugA','drugD'), 'drugB',
plotly = FALSE)