GRdrawDRC: Dose-Response Curves
In uc-bd2k/GRmetrics: Calculate growth-rate inhibition (GR) metrics

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

View source: R/GRdrawDRC.R

Given a SummarizedExperiment object created by GRfit, this function plots either the growth-rate inhibition (GR) dose response curves or the traditional dose response curves for a given set of data.

GRdrawDRC(
  fitData,
  metric = "GR",
  experiments = "all",
  min = "auto",
  max = "auto",
  points = TRUE,
  curves = TRUE,
  plotly = TRUE
)

`fitData`	an element of class SummarizedExperiment, generated by the GRfit function.
`metric`	either "GR" for GR dose response curves or "rel_cell" for traditional dose response curves based on relative cell count.
`experiments`	the names of the experiments to plot (or "all")
`min`	the minimum concentration to plot (for curves)
`max`	the maximum concentration to plot (for curves)
`points`	a logical value indicating whether points (individual GR values) will be plotted
`curves`	a logical value indicating whether sigmoidal dose-response curves will be plotted
`plotly`	a logical value indicating whether to output a ggplot2 graph or a ggplotly graph

Given a SummarizedExperiment object created by GRfit, this function plots these GR values (versus concentration) and/or the sigmoidal curves fitted to the sets of points. The results can be viewed in a static ggplot image or an interactive plotly graph.

The "min" and "max" parameters control the concentration values for which the curves are plotted. They are automatically set to the minimum and maximum concentrations of the data, but can be set by the user as well. "min" and "max" take raw values (not log transformed) for concentration.

By default, curves and points are plotted for all experiments. To specify a smaller set of experiments, use the "experiments" parameter. To see the names of individual experiments for a GRfit object fit_example, see colData(fit_example). See the examples below.

ggplot2 or ggplotly graphs of Growth-rate inhibition dose-response curves

Nicholas Clark

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

# Load Case A (example 1) input
data("inputCaseA")
# Run GRfit function with case = "A"
drc_output = GRfit(inputCaseA,
groupingVariables = c('cell_line','treatment'))
GRdrawDRC(drc_output, experiments = c('BT20 drugA', 'MCF10A drugA',
'MCF7 drugA'), min = 10^(-4), max = 10^2)
GRdrawDRC(drc_output, plotly = FALSE)