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Last data update: 2014.03.03

R: Plot individual longitudinal profiles

plotProfiles

R Documentation

Plot individual longitudinal profiles

Description

It creates a plot of individual longitudinal profiles. It is based on the output from getProfiles function.

Usage

plotProfiles(ip, data, var, trans, tvar, gvar,
             auto.layout=TRUE, lines=TRUE, points=FALSE, add=FALSE,
             xlab="Time", ylab, xaxt="s", yaxt="s", xlim, ylim, main,
             lcol, col, bg, lty=1, lwd=1, pch=21, cex.points=1,
             highlight, lines.highlight=TRUE, points.highlight=TRUE,
             lcol.highlight="red3", col.highlight="red3", bg.highlight="orange",
             lty.highlight=1, lwd.highlight=2,
             pch.highlight=23, cex.highlight=1)

Arguments

`ip`	output from `getProfiles` function containing extracted individual longitudinal profiles of each subject.
`data`	`data.frame` used to produce `ip`. It is used to detect ranges for some variables.
`var`	character string identifying the response variable to plot.
`trans`	possible transformation of the response variable.
`tvar`	character string identifying the time variable.
`gvar`	character string identifying the group variable for which different colors are used.
`auto.layout`	logical. If `TRUE`, the layout of the plotting region is determined automatically.
`lines`	logical. If `TRUE`, lines are drawn in the plot connecting observations within individuals.
`points`	logical. If `TRUE`, points are added to the plot.
`add`	logical. If `TRUE`, the new plot overlays the old one.
`lcol`	color for lines.
`col`	color for points.
`xlab, ylab, xaxt, yaxt, xlim, ylim, main, bg, lty, lwd, pch`	arguments passed to standard plotting functions. `col` might also be a vector in which case different colors are used for profiles from different groups identified by the `gvar` variable.
`cex.points`	passed as a `cex` argument to `points` function used when `points = TRUE`.
`highlight`	an optional numeric vector giving the indeces of `ip` for which the longitudinal profiles should be highlighted.
`lines.highlight`	logical. If `TRUE`, highlighting is done using lines.
`points.highlight`	logical. If `TRUE`, highlighting is done using points.
`lcol.highlight, col.highlight, bg.highlight, lty.highlight, lwd.highlight, pch.highlight, cex.highlight`	arguments `col`, `bg`, `lty`, `lwd`, `pch`, `cex` passed to `lines` and/or `points` functions which provide highlighting of selected profiles.

Value

Invisible ip.

Author(s)

Arno<c3><85><c2><a1>t Kom<c3><83><c2><a1>rek arnost.komarek[AT]mff.cuni.cz

Examples

data(PBCseq, package="mixAK")
ip <- getProfiles(t="day", y=c("age", "fdrug", "bili", "platelet", "spiders"),
                  id="id", data=PBCseq)

XLIM <- c(0, 910)
lcol2 <- c("darkgreen", "red")

oldPar <- par(mfrow=c(1, 3), bty="n")
plotProfiles(ip=ip, data=PBCseq, xlim=XLIM, var="bili", trans=log, tvar="day", gvar="fdrug",
             xlab="Time (days)", col=lcol2, auto.layout=FALSE, main="Log(bilirubin)",
             highlight=c(2, 4), col.highlight="darkblue")
plotProfiles(ip=ip, data=PBCseq, xlim=XLIM, var="platelet", tvar="day", gvar="fdrug",
             xlab="Time (days)", col=lcol2, auto.layout=FALSE, main="Platelet count",
             highlight=c(2, 4), col.highlight="darkblue")
plotProfiles(ip=ip, data=PBCseq, xlim=XLIM, var="spiders",  tvar="day", gvar="fdrug",
             xlab="Time (days)", col=lcol2, auto.layout=FALSE,
             lines=FALSE, points=TRUE,
             highlight=c(2, 4), col.highlight="darkblue", bg.highlight="skyblue") 
par(oldPar)