require(knitr) opts_chunk$set(echo = TRUE, fig.width = 5, fig.height = 4, prompt = TRUE, warning = FALSE)
require(synerdrug) data(exDrugSyn)
exDrugSyn drugNames(exDrugSyn) doses(exDrugSyn)
The data can be visualized by using plot
on the DrugSyn
object. Several visualization types are available: as heatmaps, as surface or parallel lines.
plot(exDrugSyn)
The data can be viewed as a surface by setting the type
argument of plot
to "surface"
. Arguments from persp
can be passed to plot to adjust the appearance (e.g. azimuth and co-latitude).
plot(exDrugSyn, type = "surface") plot(exDrugSyn, type = "surface", theta = -45, phi = 45)
plot(exDrugSyn, type = "parallel", ref = "drugA") plot(exDrugSyn, type = "parallel", ref = "drugB")
The single agent responses are fitted by a Hill function (also known as log-logistic model or sigmoid curve) with 4 parameters:
$$E=E_0 + \frac{E_{max}-E_0}{1 + (\frac{EC_{50}}{d})^n}$$
where:
plot(exDrugSyn, type = "ind", drug = "drugA") plot(exDrugSyn, type = "ind", drug = "drugB")
The parameters of the hill functions can be accessed with respInd
.
respInd(exDrugSyn)
Several synergy estimate idexes are computed by synerdrug
.
$HSA_{ab}=max(E_{a0}, E_{0b})/E_{ab}$;
$Bliss_{ab}=(E_{a0}+E_{0b}-E_{a0}E_{0b})/E_{ab}$
plot(exDrugSyn, type = "heatmap", what = "Bliss") plot(exDrugSyn, type = "surface", what = "LoeweExcess")
$a/A+b/B=1$
$CI_{ab}=a/A+b/B$
isobologram(exDrugSyn, effect = 0.5) isobologram(exDrugSyn, effect = 0.5, mode = "SP")
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