[R] lattice 3x3 plot: force common y-limits accross rows and align x-axes
Duncan Mackay
mackay at northnet.com.au
Tue Feb 19 04:29:23 CET 2013
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: mackay at 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(
>Â Â x=seq(1,20,by=1),
>Â Â y=seq(0.1,2,by=0.1),
>Â Â risk=gl(2,10,labels=c("low","high")),
>Â
>Â treatment=rep(gl(2,5,labels=c("oXX","oYY")),2))Â Â Â Â Â Â Â Â Â Â Â Â Â
>Â
>xyplot(y~x|treatment+risk,data=hf,type="b",
>Â Â Â Â Â Â scales=list(y=list(limits=list(c(-0.1,1.1),c(-0.1,1.1),
>Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â
>Â Â Â Â Â Â Â Â Â Â Â Â Â c(1.0,2.1),c(1.0,2.1)),
>Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â at=list(seq(0,1,0.2),NULL,
>Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â seq(1,2,0.2),NULL),
>Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â 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 Â Â Â Â Â Â Â Â Â Â Â Â Â Â
>Â risk=c("low","low","low","high","high","high"),
>Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â
>Â treatment=c("oXX","oXX","oYY","oXX","oXX","oYY"),
>Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â 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"),
>Â Â Â Â Â Â Â scales=c(y=list(limits=list(lims.low,lims.low,
>Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â
>Â Â Â Â Â Â lims.high,lims.high),
>Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â 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
>‘xlim’ or ‘ylim’ 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.berton at gene.com>
>
>Cc: "mackay at northnet.com.au"
><mackay at northnet.com.au>; "r-help at r-project.org" <r-help at 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 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.
>
>
>
>--
>
>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 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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