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Last data update: 2014.03.03

R: Panel function for bwplot that displays an entire box in the...

panel.bwplot.superpose

R Documentation

Panel function for bwplot that displays an entire box in the colors coded by groups.

Description

Panel function for bwplot that displays an entire box (central dot, box, umbrella, outliers) in the same color, coded by the groups argument. The function is based on panel.superpose.

Usage

panel.bwplot.superpose(x, y, ...,
                       groups=groups,
                       col=rep(trellis.par.get("superpose.symbol")$col,
                               length=length(groups)),
                       pch=trellis.par.get("box.dot")$pch,
                       panel.groups=panel.bwplot.groups)

panel.bwplot.groups(..., col, pch, fill, fill.alpha=NULL, group.number)

Arguments

`x, y`	Standard arguments to a lattice panel function. When `x` has class `positioned` (see `position`), the position will be forwarded by `panel.bwplot.superpose` to `panel.bwplot.groups`.
`...`	Additional lattice arguments.
`groups`	Factor to be used for color coding entire boxes: central dot, rectangle, umbrella, and outlier symbol.
`col`	Colors to be assigned to the levels of the group. The default colors are taken from `trellis.par.get("superpose.symbol")$col`.
`pch`	Standard lattice arguments. The `pch` describes the central dot. The outlier dots are specified in the `plot.symbol` component of `trellis.par.get`.
`fill, fill.alpha`	These are related to the similarly named arguments in `panel.bwplot`. The `fill` argument is ignored. It is there to capture the automatically generated `fill` argument. The default`NULL` value of `fill.alpha` implies that there is no background color for the boxes. The user can set `fill.alpha` to a number between 0 and 1. The boxes will be shaded in a lighter version of their color as implied by the `groups` argument. The value 0 gives a transparent fill, and the value one makes the box the full opaque color.
`panel.groups, group.number`	See `panel.superpose` for details.

Details

panel.bwplot.superpose is the user-level function. panel.bwplot.groups is the panel.groups function called by panel.superpose.

Author(s)

Richard M. Heiberger <rmh@temple.edu>

Examples

tmp <- data.frame(Response=rnorm(20), Group=factor(rep(LETTERS[1:3], c(5,7,8))))

bwplot(Group ~ Response, data=tmp,
       main="Default panel.bwplot, groups ignored", groups=Group)

bwplot(Group ~ Response, data=tmp,
       main="panel.bwplot.superpose",
       groups=Group, panel=panel.bwplot.superpose)

bwplot(Group ~ Response, data=tmp,
       main="panel.bwplot.superpose with fill specified",
       groups=Group, panel=panel.bwplot.superpose,
       fill.alpha=.33)


bwplot(Group ~ Response, data=tmp,
       main="panel.bwplot.superpose, with color specified",
       groups=Group, panel=panel.bwplot.superpose,
       col=c("forestgreen","blue", "brown"))


Test <- data.frame(id=rep(letters, each=4),
                   Week=rep(c(0,1,3,6), 26),
                   Treatment=rep(c("A","B"), each=52),
                   y=rep(1:4, 52) + rep(4:5, each=52) + rnorm(104))
Test$WeekTrt <- with(Test, interaction(Week, Treatment))
position(Test$Week) <- unique(Test$Week)
position(Test$WeekTrt) <- as.vector(outer(position(Test$Week), c(-.2, .2), `+`))

tapply(Test$y, Test[c("Week", "Treatment")], median)

bwplot( y ~ WeekTrt, groups = Treatment, data = Test,
      main="default panel.bwplot, groups ignored")

bwplot( y ~ WeekTrt, groups = Treatment, data = Test,
      panel=panel.bwplot.superpose,
      scales=list(x=list(limits=c(-1, 7))),
      main="Minimal use of panel.bwplot.superpose")

bwplot( y ~ WeekTrt, groups = Treatment, data = Test,
       panel=panel.bwplot.superpose,
       scales=list(x=list(limits=c(-1, 7), at=position(Test$Week))),
       box.width=.3,
       xlab="Week",
       pch=c(17, 16),
       key=list(col=trellis.par.get()$superpose.symbol$col[1:2],
           border=TRUE, title="Treatment", cex.title=1, columns=2,
           text=list(levels(Test$Treatment)),
           points=list(pch=c(17, 16))),
       par.settings=list(plot.symbol=list(pch=c(17, 16), cex=.5)),
       main="panel.bwplot.superpose with additional annotations")


bwplot( y ~ WeekTrt, groups = Treatment, data = Test,
       panel=panel.bwplot.superpose,
       scales=list(x=list(limits=c(-1, 7), at=position(Test$Week))),
       box.width=.3,
       xlab="Week",
       pch=c(17, 16),
       key=list(col=trellis.par.get()$superpose.symbol$col[1:2],
           border=TRUE, title="Treatment", cex.title=1, columns=2,
           text=list(levels(Test$Treatment)),
           points=list(pch=c(17, 16))),
       par.settings=list(plot.symbol=list(pch=c(17, 16), cex=.5)),
       main="panel.bwplot.superpose with fill and more complex panel.groups",
       panel.groups = function(...) {
           panel.stripplot(...)
           panel.bwplot.groups(...)
       },
       fill.alpha=.33,
       jitter.data = TRUE)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(HH)
Loading required package: lattice
Loading required package: grid
Loading required package: latticeExtra
Loading required package: RColorBrewer
Loading required package: multcomp
Loading required package: mvtnorm
Loading required package: survival
Loading required package: TH.data
Loading required package: MASS

Attaching package: 'TH.data'

The following object is masked from 'package:MASS':

    geyser

Loading required package: gridExtra
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/HH/panel.bwplot.superpose.Rd_%03d_medium.png", width=480, height=480)
> ### Name: panel.bwplot.superpose
> ### Title: Panel function for bwplot that displays an entire box in the
> ###   colors coded by groups.
> ### Aliases: panel.bwplot.superpose panel.bwplot.groups
> ### Keywords: dplot
> 
> ### ** Examples
> 
> tmp <- data.frame(Response=rnorm(20), Group=factor(rep(LETTERS[1:3], c(5,7,8))))
> 
> bwplot(Group ~ Response, data=tmp,
+        main="Default panel.bwplot, groups ignored", groups=Group)
> 
> bwplot(Group ~ Response, data=tmp,
+        main="panel.bwplot.superpose",
+        groups=Group, panel=panel.bwplot.superpose)
> 
> bwplot(Group ~ Response, data=tmp,
+        main="panel.bwplot.superpose with fill specified",
+        groups=Group, panel=panel.bwplot.superpose,
+        fill.alpha=.33)
> 
> 
> bwplot(Group ~ Response, data=tmp,
+        main="panel.bwplot.superpose, with color specified",
+        groups=Group, panel=panel.bwplot.superpose,
+        col=c("forestgreen","blue", "brown"))
> 
> 
> Test <- data.frame(id=rep(letters, each=4),
+                    Week=rep(c(0,1,3,6), 26),
+                    Treatment=rep(c("A","B"), each=52),
+                    y=rep(1:4, 52) + rep(4:5, each=52) + rnorm(104))
> Test$WeekTrt <- with(Test, interaction(Week, Treatment))
> position(Test$Week) <- unique(Test$Week)
> position(Test$WeekTrt) <- as.vector(outer(position(Test$Week), c(-.2, .2), `+`))
> 
> tapply(Test$y, Test[c("Week", "Treatment")], median)
    Treatment
Week        A        B
   0 4.523568 5.777646
   1 6.775678 6.782473
   3 6.453206 7.942609
   6 8.418624 8.813776
> 
> bwplot( y ~ WeekTrt, groups = Treatment, data = Test,
+       main="default panel.bwplot, groups ignored")
> 
> bwplot( y ~ WeekTrt, groups = Treatment, data = Test,
+       panel=panel.bwplot.superpose,
+       scales=list(x=list(limits=c(-1, 7))),
+       main="Minimal use of panel.bwplot.superpose")
> 
> bwplot( y ~ WeekTrt, groups = Treatment, data = Test,
+        panel=panel.bwplot.superpose,
+        scales=list(x=list(limits=c(-1, 7), at=position(Test$Week))),
+        box.width=.3,
+        xlab="Week",
+        pch=c(17, 16),
+        key=list(col=trellis.par.get()$superpose.symbol$col[1:2],
+            border=TRUE, title="Treatment", cex.title=1, columns=2,
+            text=list(levels(Test$Treatment)),
+            points=list(pch=c(17, 16))),
+        par.settings=list(plot.symbol=list(pch=c(17, 16), cex=.5)),
+        main="panel.bwplot.superpose with additional annotations")
> 
> 
> bwplot( y ~ WeekTrt, groups = Treatment, data = Test,
+        panel=panel.bwplot.superpose,
+        scales=list(x=list(limits=c(-1, 7), at=position(Test$Week))),
+        box.width=.3,
+        xlab="Week",
+        pch=c(17, 16),
+        key=list(col=trellis.par.get()$superpose.symbol$col[1:2],
+            border=TRUE, title="Treatment", cex.title=1, columns=2,
+            text=list(levels(Test$Treatment)),
+            points=list(pch=c(17, 16))),
+        par.settings=list(plot.symbol=list(pch=c(17, 16), cex=.5)),
+        main="panel.bwplot.superpose with fill and more complex panel.groups",
+        panel.groups = function(...) {
+            panel.stripplot(...)
+            panel.bwplot.groups(...)
+        },
+        fill.alpha=.33,
+        jitter.data = TRUE)
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>