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Boris.Vasiliev at forces.gc.ca

2013-Feb-15 21:54 UTC

[R] lattice 3x3 plot: force common y-limits accross rows and align x-axes

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 ####

Duncan Mackay

2013-Feb-15 23:05 UTC

head link

[R] lattice 3x3 plot: force common y-limits accross rows and align x-axes

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.

Boris Vasiliev

2013-Feb-18 16:40 UTC

head link

[R] lattice 3x3 plot: force common y-limits accross rows and align x-axes

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]]

Boris.Vasiliev at forces.gc.ca

2013-Feb-20 14:09 UTC

head link

[R] lattice 3x3 plot: force common y-limits accross rows and align x-axes

My appologies for reposting the final message in this thread.  The previous
e-mail sent from a Yahoo mailbox got completely scrubbed ...
 
 ----- Forwarded Message -----
From: Boris Vasiliev <bvasiliev@yahoo.com>
To: Duncan Mackay <mackay@northnet.com.au>;
"gunter.berton@gene.com" <gunter.berton@gene.com>;
r-help-r-project.org <r-help@r-project.org>
Sent: Tuesday, February 19, 2013 9:05:17 PM
Subject: Re: [R] lattice 3x3 plot: force common y-limits accross rows and align
x-axes


Duncan and Bert,

Thank you very much for your help with my question.  It's very much
appreciated.



I used your suggestions to get the plot I needed: 

* 3x3 lattice of dotplots, 

* x-limits are the same for all panels, 

* y-limits and y-ticks in each row are the same, 

* y-limits and y-ticks are different between rows,  

* within each row subjects are ordered by sum(count) in the row.  



My code is below just in case somebody in the r-help list finds it useful.


Regards,
Boris.


# 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'))



# create unique subjects ordered by sum(count) and risk
df$sbj.byrisk <- paste(df$risk,df$subject,sep="_")
df$sbj <- reorder(reorder(df$sbj.byrisk,df$count,sum),as.numeric(df$risk))
df$sbj.ix <- as.numeric(df$sbj)

# for each row (i.e. risk), find limits, ticks, labels, and
# maximum number of points per panel
df.byrisk <- split(df,df['risk'])
ylim <- lapply(df.byrisk,function(idf) return(range(idf$sbj.ix)))
ytck <- lapply(df.byrisk,function(idf) return(sort(unique(idf$sbj.ix))))
ylbl <- lapply(df.byrisk,function(idf) {
                          ytck <- sort(unique(idf$sbj.ix))
                          jdnx <- pmatch(ytck,idf$sbj.ix)
                          ylbl <-
sub(".*_","",idf$sbj[jdnx])
                          return(ylbl)
                        })
yhei <- unlist(lapply(ytck,length))

# set up lists for limits, ticks, labels, panel heights
ylims <- rep(ylim,c(3,3,3))
ytcks <- rep(list(NULL,NULL,NULL),c(3,3,3))
ytcks[seq(1,7,by=3)] <- ytck
ylbls <- rep(list(NULL,NULL,NULL),c(3,3,3))
ylbls[seq(1,7,by=3)] <- ylbl

# set up plot layout
laywid <- list(axis.panel=c(1,0.1,0.1))
layhei <- list(panel=yhei/sum(yhei))

# plot
oltc <- dotplot(sbj~count|treatment+risk,data=df,
                type=c("p","h"),origin=0,
                scales=list(x=list(limits=c(-1,16),
                                   alternating=FALSE),
                            y=list(relation="free",
                                   alternating=FALSE,
                                   limits=ylims,
                                   at=ytcks,
                                   labels=ylbls)),
                par.settings=list(layout.widths=laywid,
                                  layout.heights=layhei),
                between=list(y=0.2))
useOuterStrips(oltc)


________________________________

From: Duncan Mackay <mackay@northnet.com.au>
To: Boris Vasiliev <bvasiliev@yahoo.com>; r-help-r-project.org
<r-help@r-project.org>
Sent: Monday, February 18, 2013 10:29:23 PM
Subject: Re: [R] lattice 3x3 plot: force common y-limits accross rows and align
x-axes


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@northnet.com.au <mailto:mackay@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.Â  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 haveÂ  the
same y-limits; y-ticks on all panels are
'A','BB','C','DDD'.
> 
> 
> This behaviour is probably fixed by design.Â  According to documentation
for prepanel functions: "... to make this information consistent between
panels, the â€˜xlimâ€™ or â€˜ylimâ€™ 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.berton@gene.com
<mailto:gunter.berton@gene.com> >
> 
> Cc: "mackay@northnet.com.au <mailto:mackay@northnet.com.au>
" <mackay@northnet.com.au <mailto:mackay@northnet.com.au> >;
"r-help@r-project.org <mailto:r-help@r-project.org> "
<r-help@r-project.org <mailto: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.Â  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.Â
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.Â  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.Â  In the experiment,Â  not all subjects were exposed >to all
combinations of treatment and risk.Â  For each risk, I would like >to show
subject ~ count | treatment and order the subjects by the total >count.Â  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 highÂ  Â  Â  noneÂ  Â  5 >## 2Â  Â  Â  Â  A highÂ  Â  Â  optXÂ  Â  10
>## 3Â  Â  Â  Â  A highÂ  Â  Â  optZÂ  Â  2 >## 4Â  Â  Â  BB highÂ  Â  Â 
noneÂ  Â  3 >## 5Â  Â  Â  BB highÂ  Â  Â  optZÂ  Â  5 >## 6Â  Â  Â  CCC
highÂ  Â  Â  noneÂ  Â  8 >## 7Â  Â  Â  CCC highÂ  Â  Â  optXÂ  Â  1 >## 8Â
Â  Â  CCC highÂ  Â  Â  optZÂ  Â  2 >## 9Â  Â  Â  DDÂ  medÂ  Â  Â  noneÂ  Â  3
>## 10Â  Â  Â  DDÂ  medÂ  Â  Â  optZÂ  Â  7 >## 11Â  Â  Â  AÂ  medÂ  Â  Â 
noneÂ  Â  10 >## 12Â  Â  Â  AÂ  medÂ  Â  Â  optXÂ  Â
>  2 >## 13Â  Â  Â  AÂ  medÂ  Â  Â  optZÂ  Â  5 >## 14Â  Â  FFFFÂ  medÂ
Â  Â  noneÂ  Â  15 >## 15Â  Â  FFFFÂ  medÂ  Â  Â  optZ
> >Â  2 >## 16Â  Â  Â  AÂ  lowÂ  Â  Â  noneÂ  Â  7 >## 17Â  Â  Â  AÂ
lowÂ  Â  Â  optXÂ  Â  7 >## 18Â  Â  Â  BÂ  lowÂ  Â  Â  noneÂ  Â  10 >##
19Â  Â  Â  BÂ  lowÂ  Â  Â  optZÂ  Â  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().Â  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().Â  This
>  somewhat works but lattice does not >honour
> >Â  the user-defined y-limits and labels are not correct.Â  I suspect
>that it is not correct to useÂ  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$subjectx)) 
>># create dotplot and store it in oltc.{irisk} variable >oltc.irisk
<- dotplot(subjectx~count|treatment,data=df.irisk,
>layout=c(3,1),type=c('p','h'),
> >Â  >xlim=c(-1,16),origin=0, >xlab="",ylab="")
>as sign(paste('oltc.',irisk,sep=''),oltc.irisk) >} 
>># combine everthing in one plot >oltc <-
c(low=oltc.low,med=oltc.med,high=oltc.high) >pri nt(oltc) >># get rid
of variable labels in middle and right column; decrease ># distance between
columns.Â  But can't make inter-column spaces ># small enought and get
rid of the panels in all but top rows. >laywid <-
trellis.par.get('layout.widths') >laywid$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 <mailto: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 <mailto: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.







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