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.
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