1 library(lattice)
   2 library(lme4)
   3 
   4 ## data set
   5 data(sleepstudy)
   6 attach(sleepstudy)
   7 
   8 ## graphics devices
   9 quartz()                                # on OSX, interactive
  10 ## X11()                                   # on linux, interactive
  11 ## pdf()                                   # default for OSX, save to a PDF file
  12 ## png()                                   # default on Linux, save to a PNG file
  13 
  14 
  15 ## 1 variable plots
  16 histogram(Reaction)
  17 densityplot(Reaction)
  18 
  19 ## 2 variable plots
  20 barchart(Reaction ~ Days)               # wrong
  21 barchart(mean(Reaction) ~ Days)         # wrong
  22 
  23 ## aggregate data before using a barchart
  24 d <- aggregate(Reaction, by=list(Days=Days), FUN=mean)
  25 
  26 barchart(x ~ Days, d)
  27 barchart(x ~ Days, d, horizontal=FALSE) # we usually want columns
  28 
  29 
  30 ## scatter plots
  31 xyplot(Reaction ~ Days)
  32 xyplot(Reaction ~ Days, type = "l")     # line plot
  33 xyplot(Reaction ~ Days, type = "r")     # best fit linear regression line
  34 xyplot(Reaction ~ Days, type = "a")     # line plot of the average
  35 xyplot(Reaction ~ Days, type = "smooth") # smoothed line fit to the data
  36 xyplot(Reaction ~ Days, type = "p")     # points
  37 
  38 ## grouping
  39 xyplot(Reaction ~ Days, group = Subject)
  40 xyplot(Reaction ~ Days, group = Subject, auto.key=TRUE)
  41 xyplot(Reaction ~ Days, group = Subject, type = "a", auto.key=TRUE)
  42 
  43 ## panels
  44 xyplot(Reaction ~ Days | Subject)
  45 xyplot(Reaction ~ Days | Subject, type = "a")
  46 
  47 ## panels and groups
  48 ## fake up some groups
  49 d <- sleepstudy
  50 d$Condition <- rep(c(1,2))
  51 
  52 xyplot(Reaction ~ Days | Condition, group = Subject,
  53        data = d,
  54        type = "l")
  55 
  56 xyplot(Reaction ~ Days | Subject, group = Condition,
  57        data = d,
  58        type = "l")
  59 
  60 ## error bars with lattics
  61 plotting functions based on demo("intervals", package="lattice")
  62 file.show(system.file("demo/intervals.R", package = "lattice"))
  63 
  64 prepanel.ci.v <- function(x, y, ly, uy, subscripts, ...)
  65 {
  66     y <- as.numeric(y)
  67     ly <- as.numeric(ly[subscripts])
  68     uy <- as.numeric(uy[subscripts])
  69     list(ylim = range(y, uy, ly, finite = TRUE))
  70 }
  71 
  72 panel.ci.v <- function(x, y, ly, uy, subscripts, ...)
  73 {
  74     x <- as.numeric(x)
  75     y <- as.numeric(y)
  76     ly <- as.numeric(ly[subscripts])
  77     uy <- as.numeric(uy[subscripts])
  78     panel.barchart(x, y, ...)
  79     panel.arrows(x, ly, x, uy, col = 'black',
  80                  length = 0.25, unit = "native",
  81                  angle = 90, code = 3)
  82 }
  83 
  84 prepanel.ci.h <- function(x, y, lx, ux, subscripts, ...)
  85 {
  86     x <- as.numeric(x)
  87     lx <- as.numeric(lx[subscripts])
  88     ux <- as.numeric(ux[subscripts])
  89     list(xlim = range(x, ux, lx, finite = TRUE))
  90 }
  91 
  92 
  93 panel.ci.h <- function(x, y, lx, ux, subscripts, pch = 21, ...)
  94 {
  95     x <- as.numeric(x)
  96     y <- as.numeric(y)
  97     lx <- as.numeric(lx[subscripts])
  98     ux <- as.numeric(ux[subscripts])
  99     panel.abline(h = unique(y), col = "gray")
 100     panel.arrows(lx, y, ux, y, col = "black",
 101                  length = 0.25, unit = "native",
 102                  angle = 90, code = 3)
 103     panel.xyplot(x, y, pch = pch, ...)
 104 }
 105 
 106 ## once you've defined ux and lx, this will work
 107 xyplot( Reaction ~ Days | Subject,
 108        lx = lower, ux = upper,
 109        prepanel = prepanel.ci.h,
 110        panel = function (x, y, subscripts=subscripts, lx=lx, ux=ux, ...)
 111        {
 112          panel.ci.h(x, y, lx=lx, ux=ux, subscripts=subscripts,...)
 113          panel.abline(v = 0,
 114                       col = "black")
 115        })