[R] lattice 3x3 plot: force common y-limits accross rows and align x-axes
Duncan Mackay
mackay at northnet.com.au
Sat Feb 16 00:05:22 CET 2013
Hi Boris
Not sure what you mean exactly
try
library(latticeExtra)
useOuterStrips(dotplot(count ~ subject|risk*treatment,df))
if you want to change the order of the subjects in each panel and an
index column and plot the index column instead of subject and change
the scales to suit.
HTH
Duncan
Duncan Mackay
Department of Agronomy and Soil Science
University of New England
Armidale NSW 2351
Email: home: mackay at northnet.com.au
At 07:54 16/02/2013, you wrote:
>Good afternoon,
>
>I would like to ask for help in controlling y-axis limits and labels in
>lattice doplots. Unfortunately, the problem is somewhat convoluted,
>please bear with the long explanation.
>
>I would like to create a 3x3 lattice of dotplots, say subject ~ count.
>The plot is conditioned on variables treatment and risk: subject ~ count
>| treatment + risk. In the experiment, not all subjects were exposed
>to all combinations of treatment and risk. For each risk, I would like
>to show subject ~ count | treatment and order the subjects by the total
>count. At the same time, I would like the x-axes to be the same in all
>panels and aligned by columns.
>
>Here is a sample data set:
>
># raw data
>df <- data.frame(subject=c('A','A','A','BB','BB','CCC','CCC','CCC',
> 'DD','DD','A','A','A','FFFF','FFFF',
> 'A','A','B','B'),
>
>risk=c('high','high','high','high','high','high','high','high',
> 'med','med','med','med','med','med','med',
> 'low','low','low','low'),
>
>treatment=c('none','optX','optZ','none','optZ','none','optX','optZ',
>
>'none','optZ','none','optX','optZ','none','optZ',
> 'none','optX','none','optZ'),
> count=c(5,10,2,3,5,8,1,2,
> 3,7,10,2,5,15,2,
> 7,7,10,8))
># re-level factors
>df$risk <- factor(df$risk,levels=c('low','med','high'))
>df$treatment <- factor(df$treatment,levels=c('none','optX','optZ'))
>
>
>## > df
>## subject risk treatment count
>## 1 A high none 5
>## 2 A high optX 10
>## 3 A high optZ 2
>## 4 BB high none 3
>## 5 BB high optZ 5
>## 6 CCC high none 8
>## 7 CCC high optX 1
>## 8 CCC high optZ 2
>## 9 DD med none 3
>## 10 DD med optZ 7
>## 11 A med none 10
>## 12 A med optX 2
>## 13 A med optZ 5
>## 14 FFFF med none 15
>## 15 FFFF med optZ 2
>## 16 A low none 7
>## 17 A low optX 7
>## 18 B low none 10
>## 19 B low optZ 8
>
>One way to plot the data is to break-up the data into sub-frames, one
>frame for each risk, order subjects by total counts, create dotplots,
>and merge with trellis.c(). This almost works but in the merged plot I
>cannot decrease column spacing to be small enough. Also, the output of
>trellis.c() would not work with useOuterStrips() which I really like.
>My code is in TRY ONE below.
>
>Another way to create the plot is specify y-limits for each panel with
>custom prepanel and panel functions. For each panel, the data-frame for
>the panel row is isolated, subjects in the data-frame for the current
>row are ordered by counts, panel y-limits are set to the re-ordered
>levels, y-data for each panel is releveled, and data plotted with
>standard panel.dotplot(). This somewhat works but lattice does not
>honour the user-defined y-limits and labels are not correct. I suspect
>that it is not correct to use y-relation="same" in this case but "free"
>and "sliced" do not give correct results too. My code in in TRY TWO
>below.
>
>If anybody can offer any assistance with this problem, it would be much
>appreciated,
>Sincerely,
>Boris.
>
>
>#### BEGIN TRY ONE - MERGE LATTICE PLOTS ####
>library(lattice)
>library(latticeExtra)
>library(grid)
>
>for (irisk in levels(df$risk)) {
> # subset data frame
> df.irisk <- subset(df,risk==irisk)
>
> # order subjects by total count; store levels of subjectx variables
> # for later re-use in panel labels
> df.irisk$subjectx <- df.irisk$subject[,drop=TRUE]
> df.irisk$subjectx <- reorder(df.irisk$subjectx,df.irisk$count,sum)
> assign(paste('sbjx.',irisk,sep=''),levels(df.irisk$subjectx))
>
> # create dotplot and store it in oltc.{irisk} variable
> oltc.irisk <- dotplot(subjectx~count|treatment,data=df.irisk,
> layout=c(3,1),type=c('p','h'),
> xlim=c(-1,16),origin=0,
> xlab="",ylab="")
> assign(paste('oltc.',irisk,sep=''),oltc.irisk)
>}
>
># combine everthing in one plot
>oltc <- c(low=oltc.low,med=oltc.med,high=oltc.high)
>print(oltc)
>
># get rid of variable labels in middle and right column; decrease
># distance between columns. But can't make inter-column spaces
># small enought and get rid of the panels in all but top rows.
>laywid <- trellis.par.get('layout.widths')
>laywid$between <- -5
>laywid$axis.panel <- 0.7
>yscales <- list(labels=list(sbjx.low,NULL,NULL,
> sbjx.med,NULL,NULL,
> sbjx.high,NULL,NULL))
>oltd <- update(oltc,scales=list(y=yscales),
> par.settings=list(layout.widths=laywid))
>print(oltd)
>
>#### END TRY ONE - MERGE LATTICE PLOTS ####
>
>#### BEGIN TRY TWO - CUSTOM PREPANEL AND PANEL FUNCTIONS ####
>
>prepanel.dotplot.x <- function(x,y,type,subscripts,...,data=NULL) {
> # find data-frame that corresponds to the entire row of the plot
> irisk <- levels(data$risk[subscripts,drop=TRUE])
> idata <- subset(data,risk==irisk)
>
> # in the sub-frame, order subjects by total counts
> idata$subjectx <- reorder(idata$subject[,drop=TRUE],idata$count,sum)
>
> # set y-limits
> ylim <- levels(idata$subjectx)
>
> # increment packet counter and print new panel limits
> pcknum = lattice.options()$packet.counter
> lattice.options(packet.counter=pcknum+1)
> cat(paste(pcknum,":",paste(ylim,collapse=", ")),sep="\n")
> return(list(ylim=ylim))
>}
>
>panel.dotplot.x <- function(x,y,type,subscripts,...,data=NULL) {
> # get the sub-frame for the row
> irisk <- levels(data$risk[subscripts,drop=TRUE])
> idata <- subset(data,risk==irisk)
>
> # in the sub-frame, order subjects by total counts
> idata$subjectx <- reorder(idata$subject[,drop=TRUE],idata$count,sum)
>
> # re-order y-variable to "correct levels"
> y <- factor(as.character(y),levels(idata$subjectx))
>
> # print levels of the releveled subjects - should be the same
> # as the output of prepanel.dotplot.x
> pnlnum <- panel.number()
> cat(paste(pnlnum,':',paste(levels(y),collapse=", ")),sep="\n")
>
> # call standard dotplot
> panel.dotplot(x,y,...)
>}
>
># the data is plotted correctly but the labels and limits are not
>correct
>lattice.options(packet.counter=1)
>oltc <- dotplot(subject~count|treatment+risk,data=df,
> layout=c(3,3),subscripts=TRUE,
> prepanel=function(...)
>{prepanel.dotplot.x(...,data=df)},
> panel=function(...){panel.dotplot.x(...,data=df)},
> scales=list(y=list(relation='same')),
> drop.unused.levels=FALSE,
> xlim=c(0,16))
>print(oltc)
>
>#### END TRY TWO - CUSTOM PANEL AND PREPANEL FUNCTIONS ####
>
>______________________________________________
>R-help at r-project.org mailing list
>https://stat.ethz.ch/mailman/listinfo/r-help
>PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>and provide commented, minimal, self-contained, reproducible code.
More information about the R-help
mailing list