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@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.