## ----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)