plot_synergy_interaction_index: Plot interaction index with confidence intervals for observed...

In DavidQuigley/HTDoseResponseCurve: Dose Response Curve Evaluation from Incucyte and Other High-Throughput Platforms

Description

Calls code published by Lee and Kong in Statistics in Biopharmaceutical Research 2012; please cite their work if you use this function.

Usage

plot_synergy_interaction_index(ds, sample_type, treatment_1, treatment_2, hour,
  ..., log = "y", alpha = 0.05)

Arguments

ds	dataset
sample_type	sample type in ds
treatment_1	treatment in ds
treatment_2	treatment in ds
hour	hour in ds. Default 0.
...	additional parameters to pass to plot function
log	which scale should be logged; default is "y"
alpha	1-alpha is the size of the confidence intervals, default 0.05

Value

list ii: estimated interaction indices corresponding to the observations (c.d1, c.d2, E); ii.low, ii.up: estimated lower and upper CI

References

Lee & Kong Statistics in Biopharmaceutical Research 2012

Examples

dose_SCH=c(0.1, 0.5, 1, 2, 4)
eff_SCH = c(0.6701, 0.6289, 0.5577, 0.4550, 0.3755)
dose_4HPR = c(0.1, 0.5, 1, 2)
eff_4HPR = c(0.7666, 0.5833, 0.5706, 0.4934)
eff_comb = c(0.6539, 0.4919, 0.3551, 0.2341)
syn = data.frame( treatment_1 = rep("SCH66336", 13),
                  conc_1 = c( dose_SCH, rep(0, 4), dose_SCH[1:4]),
                  treatment_2 = rep("4-HPR", 13),
                  conc_2 = c( rep(0, 5), dose_4HPR, dose_4HPR ),
                  values = c(eff_SCH, eff_4HPR, eff_comb ), 
                  stringsAsFactors=FALSE )
ds_lk = create_synergy_dataset( sample_types = rep("sample_1", 13), 
                                treatments_1 = syn$treatment_1,
                                treatments_2 = syn$treatment_2,
                                concentrations_1 = syn$conc_1,
                                concentrations_2 = syn$conc_2,
                                values = syn$values)
ii=plot_synergy_interaction_index(ds=ds_lk, sample_type = "sample_1", 
                              treatment_1 = "SCH66336", treatment_2="4-HPR", 
                              hour=0, 
                              xlab="Effect", ylab="Interaction Index" ,
                              main="Interaction Index")

DavidQuigley/HTDoseResponseCurve documentation built on Jan. 23, 2021, 5:10 a.m.