Hi Boris
Just a different take on it, quick glimpse of it
library(lattice)
library(latticeExtra)
z= unique(df$subject)
df$nsub <- sapply(df$subject, pmatch, z)
useOuterStrips(xyplot(count ~
nsub|treatment*risk, df, type = "h", lwd = 2,
scales = list(x = list(at = 1:6, labels = z))))
The order can be changed by changing the order in
z by making subject a factor in the correct order
see
http://finzi.psych.upenn.edu/R/Rhelp02/archive/43626.html
on how to change the yaxis limits. An example of
mine (cut and paste) for an 8x3 panel xyplot (it
could be streamlined - i needed to change things
as I went along to get everything in)
par.settings = layout.heights =
list(panel = c(1,1,0.6,0.6,0.6,0.6,1,0.5)/sum(c(1,1,0.6,0.6,1,0.6,1,0.5)) )
),
scales = list(x = list(alternating = FALSE,
relation = "same",
rot = 0),
y = list(alternating = FALSE,
relation = "free",
limits =
list(c(-1500,30000),c(-1500,30000),c(-1500,30000), # BZ
c(-1500,30000),c(-1500,30000),c(-1500,30000),
# LV
c(-2000,20000),c(-2000,20000),c(-2000,20000),
# L2
c(
-500, 4000),c( -500, 4000),c( -500, 4000), # CL
c(-2000,20000),c(-2000,20000),c(-2000,20000),
# OP
c(-2000,20000),c(-2000,20000),c(-2000,20000),
# AB
c(-1500,30000),c(-1500,30000),c(-1500,30000),
# MO
c(-500,
4000),c(-500, 4000),c(-500, 4000)), # MX
at = rep(list(seq(0,30000,10000), NULL,
seq(0,30000,10000), NULL,
seq(0,20000,10000), NULL,
seq(0, 4000, 2000), NULL,
seq(0,20000,10000), NULL,
seq(0,20000,10000), NULL,
seq(0,30000,10000), NULL,
seq(0, 4000, 2000), NULL ),
c(1,2,
1,2, 1,2, 1,2, 1,2, 1,2, 1,2, 1,2) ),
labels =
rep(list(as.character(seq(0,30,10)), NULL,
as.character(seq(0,30,10)),
NULL,
as.character(seq(0,20,10)),
NULL,
as.character(seq(0,
4, 2)), NULL,
as.character(seq(0,20,10)),
NULL,
as.character(seq(0,20,10)),
NULL,
as.character(seq(0,30,10)),
NULL,
as.character(seq(0,
4, 2)), NULL ),
c(1,2,
1,2, 1,2, 1,2, 1,2, 1,2, 1,2, 1,2) ),
rot = 0)
),
I had different panel heights for each row so if
they were all the same it would be
panel = rep(1,n)/n
the trick is to get the rep of the lists to match
what would normally happen for each of the all
the panels ie whether an axis/label is required
str(plot object) can help if problems
HTH
Duncan
Duncan Mackay
Department of Agronomy and Soil Science
University of New England
Armidale NSW 2351
Email: home: mac...@northnet.com.au
At 12:22 19/02/2013, you wrote:
Content-Type: text/plain
Content-Disposition: inline
Content-length: 14523
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")),
Â
 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"),
              Â
 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. 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 >## 1Â Â Â Â 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 Â
2 >##
13   A med   optZ  5 >##
14  FFFF med   none  15 >## 15  FFFF med   optZ
>Â 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
>Â 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) >l
ibrary(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) >a
ssign(paste('sbjx.',irisk,sep=''),levels(df.irisk$subjectx))
>># create dotplot and store it in
oltc.{irisk} variable >oltc.irisk <-
dotplot(subjectx~count|treatment,data=df.irisk, >layout=c(3,1),type=c('p','h'),
>Â
>xlim=c(-1,16),origin=0, >xlab="",ylab="") >as
sign(paste('oltc.',irisk,sep=''),oltc.irisk) >}
>># combine everthing in one plot >oltc <-
c(low=oltc.low,med=oltc.med,high=oltc.high) >pri
nt(oltc) >># get rid of variable labels in
middle and right column; decrease ># distance
between columns. But can't make inter-column
spaces ># small enought and get rid of the
panels in all but top rows. >laywid <-
trellis.par.get('layout.widths') >laywid$between
<- -5 >laywid$axis.panel <- 0.7 >yscales <-
list(labels=list(sbjx.low,NULL,NULL, >sbjx.med,N
ULL,NULL, >sbjx.high,NULL,NULL)) >oltd <-
update(oltc,scales=list(y=yscales), >par.setting
s=list(layout.widths=laywid)) >print(oltd) >>###
# END TRY ONE - MERGE LATTICE PLOTS #### >>####
BEGIN TRY TWO - CUSTOM PREPANEL AND PANEL
FUNCTIONS #### >>prepanel.dotplot.x <-
function(x,y,type,subscripts,...,data=NULL)
{ ># find data-frame that corresponds to the entire row of the plot >irisk <-
>Â
levels(data$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()$packet.counter >lattice.option
s(packet.counter=pcknum+1) >cat(paste(pcknum,":"
,paste(ylim,collapse=",
")),sep="\n") >return(list(ylim=ylim)) >} >>pane
l.dotplot.x <-
function(x,y,type,subscripts,...,data=NULL)
{ ># get the sub-frame for the row >irisk <-
levels(data$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(level
s(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, >l
ayout=c(3,3),subscripts=TRUE, >prepanel=function
(...) >{prepanel.dotplot.x(...,data=df)}, >panel
=function(...){panel.dotplot.x(...,data=df)}, >s
cales=list(y=list(relation='same')), >drop.unuse
d.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-he
lp >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
[[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.
______________________________________________
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.
