## ----style, echo = FALSE, results = 'asis'--------------------------------- BiocStyle::markdown() ## ---- include = FALSE------------------------------------------------------ ## Case A (DRC examples) library(GRmetrics) ## -------------------------------------------------------------------------- data(inputCaseA) ## ---- include = FALSE------------------------------------------------------ inputCaseA = as.data.frame(inputCaseA) ## -------------------------------------------------------------------------- head(inputCaseA) ## ---- include = FALSE------------------------------------------------------ drc_output = GRfit(inputCaseA, groupingVariables = c('cell_line','agent')) ## -------------------------------------------------------------------------- drc_output ## -------------------------------------------------------------------------- head(GRgetMetrics(drc_output)) ## -------------------------------------------------------------------------- head(GRgetValues(drc_output)) ## -------------------------------------------------------------------------- GRgetGroupVars(drc_output) ## -------------------------------------------------------------------------- # 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) ## -------------------------------------------------------------------------- ## Case C (scatterplot and boxplot examples) data(inputCaseC) ## ---- include = FALSE------------------------------------------------------ inputCaseC = as.data.frame(inputCaseC) ## -------------------------------------------------------------------------- head(inputCaseC) ## ---- include = FALSE------------------------------------------------------ output1 = GRfit(inputData = inputCaseC, groupingVariables = c('cell_line','agent', 'perturbation', 'replicate', 'time'), case = "C") ## -------------------------------------------------------------------------- # 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)