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
On Mon, Feb 18, 2013 at 8:40 AM, Boris Vasiliev <bvasil...@yahoo.com> wrote:
> 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
> 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.
> [[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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