inst/doc/GRmetrics-vignette.R

In GRmetrics: Calculate growth-rate inhibition (GR) metrics

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BiocStyle::markdown()

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## Case A (DRC examples)
library(GRmetrics)

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data(inputCaseA)

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inputCaseA = as.data.frame(inputCaseA)

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head(inputCaseA)

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drc_output = GRfit(inputCaseA, groupingVariables = c('cell_line','agent'))

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drc_output

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head(GRgetMetrics(drc_output))

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head(GRgetValues(drc_output))

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GRgetGroupVars(drc_output)

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# Draw dose-response curves
GRdrawDRC(drc_output)
GRdrawDRC(drc_output, experiments = c('BT20 drugA', 'MCF10A drugA', 
                                      'MCF7 drugA'))
GRdrawDRC(drc_output, experiments = c('BT20 drugA', 'MCF10A drugA', 
                                      'MCF7 drugA'), 
          min = 10^(-4), max = 10^2)
GRdrawDRC(drc_output, plotly = FALSE)

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## Case C (scatterplot and boxplot examples)
data(inputCaseC)

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inputCaseC = as.data.frame(inputCaseC)

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head(inputCaseC)

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output1 = GRfit(inputData = inputCaseC, groupingVariables = 
                  c('cell_line','agent', 'perturbation', 'replicate', 'time'), 
                case = "C")

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

# Draw boxplots
GRbox(output1, metric ='GRinf', groupVariable = 'cell_line', 
      pointColor = 'agent')
GRbox(output1, metric ='GRinf', groupVariable = 'cell_line', 
      pointColor = 'agent',
      factors = c('BT20', 'MCF10A'))
GRbox(output1, metric ='GRinf', groupVariable = 'cell_line', 
      pointColor = 'agent',
      factors = c('BT20', 'MCF10A'), plotly = FALSE)
GRbox(output1, metric ='GR50', groupVariable = 'cell_line', 
      pointColor = 'agent', wilA = 'BT20', wilB = c('MCF7', 'MCF10A'),
      plotly = FALSE)