plotCurve: Curve plotting function

In mcneilco/racas: R Package for ACAS

Curve plotting function

Description

This function takes in a set of data points, curve parameters, and an equation and plots the data

Usage

plotCurve(curveData, params, fitFunction, paramNames = c("ec50", "min", "max",
  "slope"), drawIntercept = "ec50", outFile = NA, ymin = NA,
  logDose = FALSE, logResponse = FALSE, ymax = NA, xmin = NA,
  xmax = NA, height = 300, width = 300, showGrid = FALSE,
  showLegend = FALSE, showAxes = TRUE, drawCurve = TRUE,
  drawFlagged = FALSE, connectPoints = FALSE, plotMeans = FALSE,
  drawStdDevs = FALSE, addShapes = FALSE, labelAxes = FALSE,
  curveXrn = c(NA, NA), mostRecentCurveColor = NA, axes = c("x", "y"),
  ...)

Arguments

curveData	a data frame with the points with column names curveId, dose, response, flag
params	the set of parameters used to enumerate the curve
outFile	file to plot image to, if not specified then the function plots to graphic device
ymin	specify the ymin axes location
logDose	specify if x axis is in log space
logResponse	specify if y axis is in log space
ymax	specify the ymax axes location
xmin	specify the xmin axes location
xmax	specify the xmax axes location
height	height of the plot in pixels
width	width of the plot in pixels
showGrid	adds a grid to the plot
showLegend	shows a legend with curve ids on the right hand side of the plot
showAxes	turns axes on or off
drawCurve	turn the curve drawing on and off
connectPoints	will draw a line between the means of each mean X - Y
plotMeans	will plot the mean Y given a given X
drawStdDevs	will plot the Standard Deviations for each dose response combination
drawCurve	turn the curve drawing on and off

Value

If outFile is specified, then the function prints an image to the out file, if outFile is not specified, then then an image is plotted to a graphics device

Examples

LL4 <- 'min + (max - min)/((1 + exp(-hill * (log(x/ec50))))^1)'
data(curveData)
params <- curveData$parameters
curveData <- curveData$points
plotCurve(curveData, params, paramNames = c("ec50", "min", "max", "hill"), LL4, outFile = NA, ymin = NA, logDose = TRUE, ymax = NA, xmin = NA, xmax = NA, height = 300, width = 300, showGrid = FALSE, showLegend = FALSE, showAxes = TRUE)
plotCurve(curveData, params, paramNames = c("ec50", "min", "max", "hill"), LL4, outFile = NA, ymin = NA, logDose = TRUE, ymax = NA, xmin = NA, xmax = NA, height = 300, width = 300, showGrid = FALSE, showLegend = FALSE, showAxes = TRUE, plotMeans = TRUE)
plotCurve(curveData, params, paramNames = c("ec50", "min", "max", "hill"), LL4, outFile = NA, ymin = NA, logDose = TRUE, ymax = NA, xmin = NA, xmax = NA, height = 300, width = 300, showGrid = FALSE, showLegend = FALSE, showAxes = TRUE, plotMeans = TRUE, connectPoints = TRUE, drawCurve = FALSE)
plotCurve(curveData, params, paramNames = c("ec50", "min", "max", "hill"), LL4, outFile = NA, ymin = NA, logDose = TRUE, ymax = NA, xmin = NA, xmax = NA, height = 300, width = 300, showGrid = FALSE, showLegend = FALSE, showAxes = TRUE, plotMeans = TRUE, connectPoints = TRUE, drawCurve = FALSE, drawStdDevs = TRUE)

#Ki Data (using raw data)
data(kiData)
params <- kiData$parameters
points <- kiData$points
paramNames <- c("Top", "Bottom", "HotNM", "HotKDNM", "Log10Ki")
KiFCT <- 'Bottom + (Top-Bottom)/(1+10^(x-log10((10^Log10Ki)*(1+HotNM/HotKDNM))))'
plotCurve(points, params, KiFCT, paramNames, drawIntercept= "Log10Ki", outFile = NA, ymin = NA, ymax = NA, xmin = NA, xmax = NA, height = 300, width = 300, showGrid = FALSE, showLegend = FALSE, showAxes = TRUE)

#PK Curves
#PO
data(poPKCurveData)
params <- poPKCurveData$parameters
curveData <- poPKCurveData$points
plotCurve(curveData, params, paramNames = NA, outFile = NA, ymin = NA, logDose = FALSE, logResponse=TRUE, ymax = NA, xmin = NA, xmax = NA, height = 300, width = 300, showGrid = FALSE, showLegend = FALSE, showAxes = TRUE, plotMeans = FALSE, connectPoints = TRUE, drawCurve = FALSE, drawStdDevs = FALSE)
plotCurve(curveData, params, paramNames = NA, outFile = NA, ymin = NA, logDose = FALSE, logResponse=TRUE, ymax = NA, xmin = NA, xmax = NA, height = 300, width = 300, showGrid = FALSE, showLegend = FALSE, showAxes = TRUE, plotMeans = FALSE, connectPoints = TRUE, drawCurve = FALSE, drawStdDevs = FALSE, addShapes = TRUE)

#IV
data(ivPKCurveData)
params <- ivPKCurveData$parameters
curveData <- ivPKCurveData$points
plotCurve(curveData, params, paramNames = NA, outFile = NA, ymin = NA, logDose = FALSE, logResponse=TRUE, ymax = NA, xmin = NA, xmax = NA, height = 300, width = 300, showGrid = FALSE, showLegend = FALSE, showAxes = TRUE, plotMeans = FALSE, connectPoints = TRUE, drawCurve = FALSE, drawStdDevs = FALSE)
plotCurve(curveData, params, paramNames = NA, outFile = NA, ymin = NA, logDose = FALSE, logResponse=TRUE, ymax = NA, xmin = NA, xmax = NA, height = 300, width = 300, showGrid = FALSE, showLegend = FALSE, showAxes = TRUE, plotMeans = FALSE, connectPoints = TRUE, drawCurve = FALSE, drawStdDevs = FALSE, addShapes = TRUE)

#IV Overlay
data(overlayIVPKCurveData)
params <- overlayIVPKCurveData$parameters
curveData <- overlayIVPKCurveData$points
plotCurve(curveData, params, paramNames = NA, outFile = NA, ymin = NA, logDose = FALSE, logResponse=TRUE, ymax = NA, xmin = NA, xmax = NA, height = 300, width = 300, showGrid = FALSE, showLegend = FALSE, showAxes = TRUE, plotMeans = FALSE, connectPoints = TRUE, drawCurve = FALSE, drawStdDevs = FALSE)

#PO IV
data(poIVPKCurveData)
params <- poIVPKCurveData$parameters
curveData <- poIVPKCurveData$points
plotCurve(curveData, params, paramNames = NA, outFile = NA, ymin = NA, logDose = FALSE, logResponse=TRUE, ymax = NA, xmin = NA, xmax = NA, height = 300, width = 300, showGrid = FALSE, showLegend = FALSE, showAxes = TRUE, plotMeans = FALSE, connectPoints = TRUE, drawCurve = FALSE, addShapes = TRUE, drawStdDevs = TRUE)

mcneilco/racas documentation built on June 15, 2025, 5:20 a.m.