Bert,
Thank you very much for your reply. Your suggestions to set manually y-limits
of panels in lattice plot certainly puts me on the right track.
It works really well with xyplot():
hf <- data.frame(
  x=seq(1,20,by=1),
  y=seq(0.1,2,by=0.1),
  risk=gl(2,10,labels=c("low","high")),
  treatment=rep(gl(2,5,labels=c("oXX","oYY")),2))            Â
Â
xyplot(y~x|treatment+risk,data=hf,type="b",
      scales=list(y=list(limits=list(c(-0.1,1.1),c(-0.1,1.1),
                                    Â
c(1.0,2.1),c(1.0,2.1)),
                  at=list(seq(0,1,0.2),NULL,
                          seq(1,2,0.2),NULL),
                  relation="free")))
With the xyplot() above, I get 2x2 lattice where panels in the same row have
the same y-limits:
Panel 1,2 (row 1): -0.1, 1.1
Panel 3,4 (row 2): 1.0, 2.1
Unfortunately, it does not work so well with dot plots:
kf <- data.frame(subject=c("A","BB","A","C","DDD","DDD"),
                risk=c("low","low","low","high","high","high"),
               Â
treatment=c("oXX","oXX","oYY","oXX","oXX","oYY"),
                count=c(5,7,10,4,13,8))
kf$risk <- factor(kf$risk,levels=c("low","high"))
kf$treatment <- factor(kf$treatment,levels=c("oXX","oYY"))
lims.low <- factor(c("A","BB"))
lims.high <- factor(c("C","DDD"))
dotplot(subject~count|treatment+risk,data=kf,type=c("p","h"),
       scales=c(y=list(limits=list(lims.low,lims.low,
                             Â
lims.high,lims.high),
                       relation="free")))
With the dotplot() above I get 2x2 lattice plot where all panels have the
same y-limits; y-ticks on all panels are 'A','BB','C','DDD'.
This behaviour is probably fixed by design. According to documentation for
prepanel functions: "... to make this information consistent between panels,
the âxlimâ or âylimâ values should represent all the levels of the
corresponding factor, even if some are not used within that particular panel."
A way to trick lattice would be to use xyplot() with a custom panel function.Â
I'll give a try today or tomorrow.
Regards,
Boris.
________________________________
From: Bert Gunter <gunter.ber...@gene.com>
Cc: "mac...@northnet.com.au" <mac...@northnet.com.au>; "r-help@r-project.org"
<r-help@r-project.org>
Sent: Monday, February 18, 2013 1:09:10 PM
Subject: Re: [R] lattice 3x3 plot: force common y-limits accross rows and align
x-axes
Boris:
If I understand you correctly, you wish to set panel limits by row. I
know of no "slick" way of doing this (others may), as what is in a row
can change depending on layout and how you determine the scale for the
rows' contents may depend on the application context.
So I would do it manually: First, outside of trellis, compute your
xlim and ylim values for each row as you desire. Then issue the
trellis call, with the relation="free" component in the scales = list,
Then just use the list form of the xlim and ylim argument to xyplot
with your precomputed limits.
-- Bert
> 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',
>Â >'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 >##Â Â
>subject risk treatment count >## 1    A high   none  5 >##
>2    A high   optX  10 >## 3    A high   optZÂ
>  2 >## 4   BB high   none  3 >## 5   BB high Â
> optZ  5 >## 6   CCC high   none  8 >## 7   CCC
>high   optX  1 >## 8   CCC high   optZ  2 >## 9Â
>  DD med   none  3 >## 10   DD med   optZ Â
> 7 >## 11   A med   none  10 >## 12   A med  Â
> optXÂ Â
2 >## 13   A med   optZ  5 >## 14  FFFF med  Â
none  15 >## 15  FFFF med   optZ
> 2 >## 16   A low   none  7 >## 17   A low Â
>  optX  7 >## 18   B low   none  10 >## 19  Â
>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.Â
>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.Â
>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$subjectx)) >># create
>dotplot and store it in oltc.{irisk} variable >oltc.irisk <-
>dotplot(subjectx~count|treatment,data=df.irisk, >layout=c(3,1),type=c('p','h'),
>Â >xlim=c(-1,16),origin=0, >xlab="",ylab="")
>>assign(paste('oltc.',irisk,sep=''),oltc.irisk) >} >># combine everthing in
>one plot >oltc <- c(low=oltc.low,med=oltc.med,high=oltc.high) >print(oltc) >>#
>get rid of variable labels in middle and right column; decrease ># distance
>between columns. But can't make inter-column spaces ># small enought and get
>rid of the panels in all but top rows. >laywid <-
>trellis.par.get('layout.widths') >laywid$between <- -5 >laywid$axis.panel <-
>0.7 >yscales <- list(labels=list(sbjx.low,NULL,NULL, >sbjx.med,NULL,NULL,
>>sbjx.high,NULL,NULL)) >oltd <- update(oltc,scales=list(y=yscales),
>>par.settings=list(layout.widths=laywid)) >print(oltd) >>#### END TRY ONE -
>MERGE LATTICE PLOTS #### >>#### BEGIN TRY TWO - CUSTOM PREPANEL AND PANEL
>FUNCTIONS #### >>prepanel.dotplot.x <-
>function(x,y,type,subscripts,...,data=NULL) { ># find data-frame that
>corresponds to the entire row of the plot >irisk <-
>Â levels(data$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
>Â 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.
>Â Â Â Â [[alternative HTML version deleted]]
>
> ______________________________________________
> 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.
--
Bert Gunter
Genentech Nonclinical Biostatistics
Internal Contact Info:
Phone: 467-7374
Website:
http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm
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