R/timeEventPlot.R
In MangoTheCat/RNMGraphics: NONMEM graphics
#' Generates dot plots of dosing events against time for each individual in a NONMEM object.
#' @name timeEventDPlot
#' @title NONMEM Time to Event Dot Plot
#' @param obj An object of class \code{NMRun}, \code{NMProblem}, or \code{data.frame}. The object from which data will be plotted.
#' @param tVar Time variable.
#' @param doseVar Dosing amount identifier variable.
#' @param evtVar Event identifier variable.
#' @param iVar Subject identifier variable.
#' @param title Main title
#' @param xLab x-axis label
#' @param yLab y-axis label
#' @param addLegend Should legends be added?
#' @param problemNum The problem required for a \code{NMRun} object.
#' @param subProblems The sub problem of a run with simulations.
#' @param ...
#' @return Multitrellis class object containing the plot.
#' @author Mango Solutions
#' @examples
#' \dontrun{
#' Theoph2 <- as.data.frame(transform(Theoph, Evt = as.numeric((Time == 0)) ))
#' timeEventDPlot(Theoph2, tVar = "Time", concVar = "conc",
#' doseVar = "Dose", evtVar = "Evt", iVar = "Subject")
#' }
#' @keywords hplot
#' @exportMethod timeEventDPlot
timeEventDPlot<- function(obj, tVar = "TIME", doseVar = "AMT",
evtVar = "EVID", iVar = "ID",title = "Time to event", xLab = "TIME", yLab = "ID",
addLegend = TRUE, problemNum = 1, subProblems = 1, ...)
{
RNMGraphicsStop("Not implemented for this class\n")
}
timeEventDPlot.NMRun <- function(obj, tVar = "TIME", doseVar = "AMT",
evtVar = "EVID", iVar = "ID",title = "Time to event", xLab = "TIME",
yLab = "ID", addLegend = TRUE, problemNum = 1, subProblems = 1, ...)
{
prob <- getProblem(obj, problemNum)
x <- as.list(match.call())
x$obj <- prob
do.call(timeEventDPlot, x[-1])
}
timeEventDPlot.NMProblem <- function(obj, tVar = "TIME", doseVar = "AMT",
evtVar = "EVID", iVar = "ID",title = "Time to event", xLab = "TIME",
yLab = "ID", addLegend = TRUE, problemNum = 1, subProblems = 1, ...)
{
dataSet <- nmData(obj, subProblemNum = subProblems)
graphSubset(dataSet) <- graphSubset(obj)
x <- as.list(match.call())
x$obj <- dataSet
do.call(timeEventDPlot, x[-1])
}
timeEventDPlot.data.frame <- function(obj, tVar = "TIME", doseVar = "AMT",
evtVar = "EVID", iVar = "ID",title = "Time to event", xLab = "TIME", yLab = "ID",
addLegend = TRUE, problemNum = 1, subProblems = 1, ...)
{
nmDotPlot(obj, factVar = iVar, contVar = tVar, gVar = evtVar, xLabs = xLab, yLabs = yLab, addLegend = addLegend,
title = title, problemNum = 1, subProblems = 1, ...)
}
setGeneric("timeEventDPlot")
setMethod("timeEventDPlot", signature(obj = "data.frame"), timeEventDPlot.data.frame)
setMethod("timeEventDPlot", signature(obj = "NMRun"), timeEventDPlot.NMRun)
setMethod("timeEventDPlot", signature(obj = "NMProblem"), timeEventDPlot.NMProblem)
#' Generate scatter plot of concentration/DV against time for each individual in
#' a NONMEM object. These will be line plots, with vertical reference lines at dosing times
#' @name timeEventSPlot
#' @title NONMEM Time to Event Scatter Plot
#' @param obj An object of class \code{NMRun}, \code{NMProblem}, or \code{data.frame}. The object from which data will be plotted.
#' @param concVar Dependent variable.
#' @param tVar Time variable.
#' @param doseVar Dosing amount variable.
#' @param evtVar Event identifier variable.
#' @param iVar Subject identifier variable.
#' @param subjectNum A vector of subject numbers. Otherwise, all subject numbers are plotted.
#' @param title Main title
#' @param xLab X-axis label
#' @param yLab Y-axis label
#' @param layout Numeric vector giving the number of columns, rows and pages in a multipanel display
#' @param maxPanels Maximum number of panels to display on each page
#' @param problemNum The problem required for a \code{NMRun} object
#' @param subProblems The sub problem of a run with simulations
#' @param yAxisScaleRelations Y-axis scale relations when panels are displayed. One of \code{"same"}, \code{"free"} or \code{"sliced"}.
#' @param xAxisScaleRelations X-axis scale relations when panels are displayed. One of \code{"same"}, \code{"free"} or \code{"sliced"}.
#' @param expX Logical flag. Exponentiate x-axis variable?
#' @param expY Logical flag. Exponentiate the y-axis variables?
#' @param xRotAngle Single numeric. Angle by which to rotate
#' @param ... Additional parameters to xyplot
#' @return Multitrellis class object containing the plot.
#' @author Mango Solutions
#' @examples
#' \dontrun{
#' Theoph2 <- as.data.frame(transform(Theoph, Evt = as.numeric((Time == 0)) ))
#' timeEventSPlot(Theoph2, tVar = "Time", concVar = "conc",
#' doseVar = "Dose", evtVar = "Evt", iVar = "Subject")
#' }
#' @keywords hplot
#' @exportMethod timeEventSPlot
timeEventSPlot <- function(obj, concVar = "DV", tVar = "TIME", doseVar = "AMT",
evtVar = "EVID", iVar = "ID", subjectNum = NULL,
title = NULL, xLab = NULL, yLab = NULL,
layout = NULL, maxPanels = NULL,
problemNum = 1, subProblems = 1, xAxisScaleRelations = c("same","free","sliced"),
yAxisScaleRelations = c("same","free","sliced"),
expX = FALSE, expY = FALSE, xRotAngle = 0,
...)
{
RNMGraphicsStop("Not implemented for this class\n")
}
panel.timeEventSPlot <- function(x, y, subscripts, doseInfo, colNames = c("tVar" = "TIME",
"doseVar" = "AMT", "evtVar" = "EVID"), ...)
{
panel.xyplot(x, y, subscripts = subscripts, ...)
doseInfo <- doseInfo[subscripts,][doseInfo[[colNames["evtVar"]]] != 0,]
panel.abline(v = doseInfo[,colNames["tVar"]], col = "black", lty = 2)
}
timeEventSPlot.NMRun <- function(obj, concVar = "DV", tVar = "TIME", doseVar = "AMT",
evtVar = "EVID", iVar = "ID", subjectNum = NULL,
title = NULL, xLab = NULL, yLab = NULL,
layout = NULL, maxPanels = NULL,
problemNum = 1, subProblems = 1, xAxisScaleRelations = c("same","free","sliced"),
yAxisScaleRelations = c("same","free","sliced"),
expX = FALSE, expY = FALSE, xRotAngle = 0,
...)
{
prob <- getProblem(obj, problemNum)
x <- as.list(match.call())
x$obj <- prob
do.call(timeEventSPlot, x[-1])
}
timeEventSPlot.NMProblem <- function(obj, concVar = "DV", tVar = "TIME", doseVar = "AMT",
evtVar = "EVID", iVar = "ID", subjectNum = NULL,
title = NULL, xLab = NULL, yLab = NULL,
layout = NULL, maxPanels = NULL,
problemNum = 1, subProblems = 1,
xAxisScaleRelations = c("same","free","sliced"),
yAxisScaleRelations = c("same","free","sliced"),
expX = FALSE, expY = FALSE, xRotAngle = 0,
...)
{
dataSet <- nmData(obj, subProblemNum = subProblems)
graphSubset(dataSet) <- graphSubset(obj)
x <- as.list(match.call())
x$obj <- dataSet
do.call(timeEventSPlot, x[-1])
}
timeEventSPlot.data.frame <- function(obj, concVar = "DV", tVar = "TIME", doseVar = "AMT",
evtVar = "EVID", iVar = "ID", subjectNum = NULL,
title = NULL, xLab = NULL, yLab = NULL, layout = NULL, maxPanels = NULL,
problemNum = 1, subProblems = 1,
xAxisScaleRelations = c("same","free","sliced"),
yAxisScaleRelations = c("same","free","sliced"),
expX = FALSE, expY = FALSE, xRotAngle = 0, ...)
{
obj <- applyGraphSubset(obj)
if(is.null(xLab)) xLab <- "Time"
if(is.null(yLab)) yLab <- "Concentration"
if(is.null(title)) title <- "Concentration vs Time"
if(is.null(subjectNum)) subjectNum <- unique(obj[[iVar]])
if(length(maxPanels) > 0) layout <- NULL
# ensure that maxPanels is numeric, even if empty
else maxPanels <- numeric(0)
# create plotting formula
form <- paste(concVar, tVar, sep = "~")
form <- paste(form, iVar, sep = "|")
# subset the object
obj <- obj[obj[[iVar]] %in% subjectNum,]
obj[[iVar]] <- as.factor(obj[[iVar]])
doses <- obj[c(doseVar, evtVar, tVar)]
varMapping = c("tVar" = tVar, "doseVar" = doseVar, "evtVar" = evtVar)
graphParams <- getAllGraphParams()
plotKey <- list(text = list(c("Concentration", "Dose"), space = "right"),
lines = list(lty = 1:2, col = c(graphParams$plot.line$col, "black")), cex = 0.7)
# set the scales to implement xRotAngle and *AxisScaleRelations
scales <- list(x = list( rot = xRotAngle, relation = match.arg(xAxisScaleRelations) ),
y = list(relation = match.arg(yAxisScaleRelations)))
objModified <- obj
if(expX)
{
expXVar <- try(exp(obj[,tVar]), silent = TRUE)
if(is(expXVar, "try-error"))
{
# this shouldn't be possible when invoked from application front-end
RNMGraphicsStop("Unable to exponentiate time variable")
}
objModified[,tVar] <- expXVar
}
if(expY)
{
expYVars <- try(exp(obj[,concVar]), silent = TRUE)
if(is(expYVars, "try-error"))
{
# this shouldn't be possible when invoked from application front-end
RNMGraphicsStop("Unable to exponentiate dependent variable")
}
objModified[,concVar] <- expYVars
}
plt <- with(graphParams,
xyplot(as.formula(form), type = "l", data = objModified,
par.settings = list(
plot.symbol = plot.symbol,
par.xlab.text = axis.text, par.ylab.text = axis.text,
par.main.text = title.text, plot.line = plot.line,
add.line = refline, strip.background = strip.bg,
layout.widths = layout.widths, layout.heights = layout.heights),
strip = strip$stripfun, panel = panel.timeEventSPlot, doseInfo = doses, colNames = varMapping,
xlab = xLab, ylab = yLab, main = title,
key = plotKey , layout = layout, scales = scales, ...) )
multiTrellis(list(plt), maxPanels = maxPanels)
# plt
}
setGeneric("timeEventSPlot")
setMethod("timeEventSPlot", signature(obj = "data.frame"), timeEventSPlot.data.frame)
setMethod("timeEventSPlot", signature(obj = "NMRun"), timeEventSPlot.NMRun)
setMethod("timeEventSPlot", signature(obj = "NMProblem"), timeEventSPlot.NMProblem)
MangoTheCat/RNMGraphics documentation built on May 8, 2019, 3:51 p.m.
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#' Generates dot plots of dosing events against time for each individual in a NONMEM object.
#' @name timeEventDPlot
#' @title NONMEM Time to Event Dot Plot
#' @param obj An object of class \code{NMRun}, \code{NMProblem}, or \code{data.frame}. The object from which data will be plotted.
#' @param tVar Time variable.
#' @param doseVar Dosing amount identifier variable.
#' @param evtVar Event identifier variable.
#' @param iVar Subject identifier variable.
#' @param title Main title
#' @param xLab x-axis label
#' @param yLab y-axis label
#' @param addLegend Should legends be added?
#' @param problemNum The problem required for a \code{NMRun} object.
#' @param subProblems The sub problem of a run with simulations.
#' @param ...
#' @return Multitrellis class object containing the plot.
#' @author Mango Solutions
#' @examples
#' \dontrun{
#' Theoph2 <- as.data.frame(transform(Theoph, Evt = as.numeric((Time == 0)) ))
#' timeEventDPlot(Theoph2, tVar = "Time", concVar = "conc",
#' doseVar = "Dose", evtVar = "Evt", iVar = "Subject")
#' }
#' @keywords hplot
#' @exportMethod timeEventDPlot
timeEventDPlot<- function(obj, tVar = "TIME", doseVar = "AMT",
evtVar = "EVID", iVar = "ID",title = "Time to event", xLab = "TIME", yLab = "ID",
addLegend = TRUE, problemNum = 1, subProblems = 1, ...)
{
RNMGraphicsStop("Not implemented for this class\n")
}
timeEventDPlot.NMRun <- function(obj, tVar = "TIME", doseVar = "AMT",
evtVar = "EVID", iVar = "ID",title = "Time to event", xLab = "TIME",
yLab = "ID", addLegend = TRUE, problemNum = 1, subProblems = 1, ...)
{
prob <- getProblem(obj, problemNum)
x <- as.list(match.call())
x$obj <- prob
do.call(timeEventDPlot, x[-1])
}
timeEventDPlot.NMProblem <- function(obj, tVar = "TIME", doseVar = "AMT",
evtVar = "EVID", iVar = "ID",title = "Time to event", xLab = "TIME",
yLab = "ID", addLegend = TRUE, problemNum = 1, subProblems = 1, ...)
{
dataSet <- nmData(obj, subProblemNum = subProblems)
graphSubset(dataSet) <- graphSubset(obj)
x <- as.list(match.call())
x$obj <- dataSet
do.call(timeEventDPlot, x[-1])
}
timeEventDPlot.data.frame <- function(obj, tVar = "TIME", doseVar = "AMT",
evtVar = "EVID", iVar = "ID",title = "Time to event", xLab = "TIME", yLab = "ID",
addLegend = TRUE, problemNum = 1, subProblems = 1, ...)
{
nmDotPlot(obj, factVar = iVar, contVar = tVar, gVar = evtVar, xLabs = xLab, yLabs = yLab, addLegend = addLegend,
title = title, problemNum = 1, subProblems = 1, ...)
}
setGeneric("timeEventDPlot")
setMethod("timeEventDPlot", signature(obj = "data.frame"), timeEventDPlot.data.frame)
setMethod("timeEventDPlot", signature(obj = "NMRun"), timeEventDPlot.NMRun)
setMethod("timeEventDPlot", signature(obj = "NMProblem"), timeEventDPlot.NMProblem)
#' Generate scatter plot of concentration/DV against time for each individual in
#' a NONMEM object. These will be line plots, with vertical reference lines at dosing times
#' @name timeEventSPlot
#' @title NONMEM Time to Event Scatter Plot
#' @param obj An object of class \code{NMRun}, \code{NMProblem}, or \code{data.frame}. The object from which data will be plotted.
#' @param concVar Dependent variable.
#' @param tVar Time variable.
#' @param doseVar Dosing amount variable.
#' @param evtVar Event identifier variable.
#' @param iVar Subject identifier variable.
#' @param subjectNum A vector of subject numbers. Otherwise, all subject numbers are plotted.
#' @param title Main title
#' @param xLab X-axis label
#' @param yLab Y-axis label
#' @param layout Numeric vector giving the number of columns, rows and pages in a multipanel display
#' @param maxPanels Maximum number of panels to display on each page
#' @param problemNum The problem required for a \code{NMRun} object
#' @param subProblems The sub problem of a run with simulations
#' @param yAxisScaleRelations Y-axis scale relations when panels are displayed. One of \code{"same"}, \code{"free"} or \code{"sliced"}.
#' @param xAxisScaleRelations X-axis scale relations when panels are displayed. One of \code{"same"}, \code{"free"} or \code{"sliced"}.
#' @param expX Logical flag. Exponentiate x-axis variable?
#' @param expY Logical flag. Exponentiate the y-axis variables?
#' @param xRotAngle Single numeric. Angle by which to rotate
#' @param ... Additional parameters to xyplot
#' @return Multitrellis class object containing the plot.
#' @author Mango Solutions
#' @examples
#' \dontrun{
#' Theoph2 <- as.data.frame(transform(Theoph, Evt = as.numeric((Time == 0)) ))
#' timeEventSPlot(Theoph2, tVar = "Time", concVar = "conc",
#' doseVar = "Dose", evtVar = "Evt", iVar = "Subject")
#' }
#' @keywords hplot
#' @exportMethod timeEventSPlot
timeEventSPlot <- function(obj, concVar = "DV", tVar = "TIME", doseVar = "AMT",
evtVar = "EVID", iVar = "ID", subjectNum = NULL,
title = NULL, xLab = NULL, yLab = NULL,
layout = NULL, maxPanels = NULL,
problemNum = 1, subProblems = 1, xAxisScaleRelations = c("same","free","sliced"),
yAxisScaleRelations = c("same","free","sliced"),
expX = FALSE, expY = FALSE, xRotAngle = 0,
...)
{
RNMGraphicsStop("Not implemented for this class\n")
}
panel.timeEventSPlot <- function(x, y, subscripts, doseInfo, colNames = c("tVar" = "TIME",
"doseVar" = "AMT", "evtVar" = "EVID"), ...)
{
panel.xyplot(x, y, subscripts = subscripts, ...)
doseInfo <- doseInfo[subscripts,][doseInfo[[colNames["evtVar"]]] != 0,]
panel.abline(v = doseInfo[,colNames["tVar"]], col = "black", lty = 2)
}
timeEventSPlot.NMRun <- function(obj, concVar = "DV", tVar = "TIME", doseVar = "AMT",
evtVar = "EVID", iVar = "ID", subjectNum = NULL,
title = NULL, xLab = NULL, yLab = NULL,
layout = NULL, maxPanels = NULL,
problemNum = 1, subProblems = 1, xAxisScaleRelations = c("same","free","sliced"),
yAxisScaleRelations = c("same","free","sliced"),
expX = FALSE, expY = FALSE, xRotAngle = 0,
...)
{
prob <- getProblem(obj, problemNum)
x <- as.list(match.call())
x$obj <- prob
do.call(timeEventSPlot, x[-1])
}
timeEventSPlot.NMProblem <- function(obj, concVar = "DV", tVar = "TIME", doseVar = "AMT",
evtVar = "EVID", iVar = "ID", subjectNum = NULL,
title = NULL, xLab = NULL, yLab = NULL,
layout = NULL, maxPanels = NULL,
problemNum = 1, subProblems = 1,
xAxisScaleRelations = c("same","free","sliced"),
yAxisScaleRelations = c("same","free","sliced"),
expX = FALSE, expY = FALSE, xRotAngle = 0,
...)
{
dataSet <- nmData(obj, subProblemNum = subProblems)
graphSubset(dataSet) <- graphSubset(obj)
x <- as.list(match.call())
x$obj <- dataSet
do.call(timeEventSPlot, x[-1])
}
timeEventSPlot.data.frame <- function(obj, concVar = "DV", tVar = "TIME", doseVar = "AMT",
evtVar = "EVID", iVar = "ID", subjectNum = NULL,
title = NULL, xLab = NULL, yLab = NULL, layout = NULL, maxPanels = NULL,
problemNum = 1, subProblems = 1,
xAxisScaleRelations = c("same","free","sliced"),
yAxisScaleRelations = c("same","free","sliced"),
expX = FALSE, expY = FALSE, xRotAngle = 0, ...)
{
obj <- applyGraphSubset(obj)
if(is.null(xLab)) xLab <- "Time"
if(is.null(yLab)) yLab <- "Concentration"
if(is.null(title)) title <- "Concentration vs Time"
if(is.null(subjectNum)) subjectNum <- unique(obj[[iVar]])
if(length(maxPanels) > 0) layout <- NULL
# ensure that maxPanels is numeric, even if empty
else maxPanels <- numeric(0)
# create plotting formula
form <- paste(concVar, tVar, sep = "~")
form <- paste(form, iVar, sep = "|")
# subset the object
obj <- obj[obj[[iVar]] %in% subjectNum,]
obj[[iVar]] <- as.factor(obj[[iVar]])
doses <- obj[c(doseVar, evtVar, tVar)]
varMapping = c("tVar" = tVar, "doseVar" = doseVar, "evtVar" = evtVar)
graphParams <- getAllGraphParams()
plotKey <- list(text = list(c("Concentration", "Dose"), space = "right"),
lines = list(lty = 1:2, col = c(graphParams$plot.line$col, "black")), cex = 0.7)
# set the scales to implement xRotAngle and *AxisScaleRelations
scales <- list(x = list( rot = xRotAngle, relation = match.arg(xAxisScaleRelations) ),
y = list(relation = match.arg(yAxisScaleRelations)))
objModified <- obj
if(expX)
{
expXVar <- try(exp(obj[,tVar]), silent = TRUE)
if(is(expXVar, "try-error"))
{
# this shouldn't be possible when invoked from application front-end
RNMGraphicsStop("Unable to exponentiate time variable")
}
objModified[,tVar] <- expXVar
}
if(expY)
{
expYVars <- try(exp(obj[,concVar]), silent = TRUE)
if(is(expYVars, "try-error"))
{
# this shouldn't be possible when invoked from application front-end
RNMGraphicsStop("Unable to exponentiate dependent variable")
}
objModified[,concVar] <- expYVars
}
plt <- with(graphParams,
xyplot(as.formula(form), type = "l", data = objModified,
par.settings = list(
plot.symbol = plot.symbol,
par.xlab.text = axis.text, par.ylab.text = axis.text,
par.main.text = title.text, plot.line = plot.line,
add.line = refline, strip.background = strip.bg,
layout.widths = layout.widths, layout.heights = layout.heights),
strip = strip$stripfun, panel = panel.timeEventSPlot, doseInfo = doses, colNames = varMapping,
xlab = xLab, ylab = yLab, main = title,
key = plotKey , layout = layout, scales = scales, ...) )
multiTrellis(list(plt), maxPanels = maxPanels)
# plt
}
setGeneric("timeEventSPlot")
setMethod("timeEventSPlot", signature(obj = "data.frame"), timeEventSPlot.data.frame)
setMethod("timeEventSPlot", signature(obj = "NMRun"), timeEventSPlot.NMRun)
setMethod("timeEventSPlot", signature(obj = "NMProblem"), timeEventSPlot.NMProblem)
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