lattice 3x3 plot: force common y-limits accross rows and align x-axes

Hi Duncan,

Thank you for quick reply.

I am not sure that your solution solves the problem.  If I use
useOuterStrips(dotplot(count ~ subject|risk*treatment,df))
the order of subjects and panel y-limits in each panel are

A, B, BB, CCC, DD, FFFF.

However, the order of subjects and y-limits which I would
like to get are

Panels 1,2,3 (row 1): A, B

Panels 4,5,6 (row 2): DD, A, FFFF

Panels 7,8,9 (row 3): BB, CCC, A.

I can re-index subjects so that they have correct order in each row.
However, I am not sure how to specify per-panel y-limits in lattice
so that all panels in the same row have the same y-limits irrespective
of what data is in these panels.

With relation "same", the limits are the same for all plots; with
relation "free" the limits depend on the data in the panel.  I thought
that relation "free" and specification of y-limits via prepanel
function (my previous trys) or as a list would do the trick:
scales=list(y=list(limits=list(panel-1-limits, panel-2-limits, ...))
but I cannot get it to work.

I guess I am missing something basic ... any ideas or advice to give
up are greatly appreciated.

Regards,
Boris.



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