Re: [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 bvasil...@yahoo.com
To: Duncan Mackay mac...@northnet.com.au; gunter.ber...@gene.com
gunter.ber...@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',
'','',
'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 mac...@northnet.com.au
To: Boris Vasiliev bvasil...@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
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,Â
* within each row subjects are ordered by sum(count) in the row.Â
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',
                 '','',
                 '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$sbj[jdnx])
                         return(ylbl)
                       })
yhei - unlist(lapply(ytck,length))
# set up lists for limits, ticks, labels, panel heights
ylims - rep(ylim,c(3,3,3))
ytcks - rep(list(NULL,NULL,NULL),c(3,3,3))
ytcks[seq(1,7,by=3)] - ytck
ylbls - rep(list(NULL,NULL,NULL),c(3,3,3))
ylbls[seq(1,7,by=3)] - ylbl
# set up plot layout
laywid - list(axis.panel=c(1,0.1,0.1))
layhei - list(panel=yhei/sum(yhei))
# plot
oltc - dotplot(sbj~count|treatment+risk,data=df,
               type=c(p,h),origin=0,
               scales=list(x=list(limits=c(-1,16),
                                 Â
alternating=FALSE),
                           y=list(relation=free,
                                 Â
alternating=FALSE,
                                 Â
limits=ylims,
                                  at=ytcks,
                                 Â
labels=ylbls)),
               par.settings=list(layout.widths=laywid,
                                Â
layout.heights=layhei),
               between=list(y=0.2))
useOuterStrips(oltc)
From: Duncan Mackay mac...@northnet.com.au
oject.org
Sent: Monday, February 18, 2013 10:29:23 PM
Subject: Re: [R] lattice 3x3 plot: force common y-limits accross rows and
align x-axes
Hi Boris
Just a different take on it, quick glimpse of it
library(lattice)
library(latticeExtra)
z= unique(df$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
[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, .
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,
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','','', '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 ## 1A high none 5 ## 2A high
optX10 ## 3A 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 none10 ## 12 A med optX 2 ## 13
A med optZ 5 ## 14 med none15 ## 15
med optZ
2 ## 16 A low none 7 ## 17 A low optX 7 ##
18 B low none10 ## 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
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
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, .
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,
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','','', '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 ## 1A high none 5 ## 2A high
optX10 ## 3A 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 none10 ## 12 A med optX 2 ## 13
A med optZ 5 ## 14 med none15 ## 15
med optZ
2 ## 16 A low none 7 ## 17 A low optX 7
## 18 B low none10 ## 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
Re: [R] lattice 3x3 plot: force common y-limits accross rows and align x-axes
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)),   treatment=rep(gl(2,5,labels=c(oXX,oYY)),2))              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),                                      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),                 risk=c(low,low,low,high,high,high),                 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,                               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, . 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, 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
Re: [R] lattice 3x3 plot: force common y-limits accross rows and align x-axes
, 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, .
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,
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','','', '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
[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','','',
'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$treatment,levels=c('none','optX','optZ'))
## df
##subject risk treatment count
## 1A high none 5
## 2A high optX10
## 3A high optZ 2
## 4 BB high none 3
## 5 BB high optZ 5
## 6 CCC high none 8
## 7 CCC high optX 1
## 8 CCC high optZ 2
## 9 DD med none 3
## 10 DD med optZ 7
## 11 A med none10
## 12 A med optX 2
## 13 A med optZ 5
## 14 med none15
## 15 med optZ 2
## 16 A low none 7
## 17 A low optX 7
## 18 B low none10
## 19 B low optZ 8
One way to plot the data is to break-up the data into sub-frames, one
frame for each risk, order subjects by total counts, create dotplots,
and merge with trellis.c(). This almost works but in the merged plot I
cannot decrease column spacing to be small enough. Also, the output of
trellis.c() would not work with useOuterStrips() which I really like.
My code is in TRY ONE below.
Another way to create the plot is specify y-limits for each panel with
custom prepanel and panel functions. For each panel, the data-frame for
the panel row is isolated, subjects in the data-frame for the current
row are ordered by counts, panel y-limits are set to the re-ordered
levels, y-data for each panel is releveled, and data plotted with
standard panel.dotplot(). This somewhat works but lattice does not
honour the user-defined y-limits and labels are not correct. I suspect
that it is not correct to use y-relation=same in this case but free
and sliced do not give correct results too. My code in in TRY TWO
below.
If anybody can offer any assistance with this problem, it would be much
appreciated,
Sincerely,
Boris.
BEGIN TRY ONE - MERGE LATTICE PLOTS
library(lattice)
library(latticeExtra)
library(grid)
for (irisk in levels(df$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
Re: [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: mac...@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','','',
'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
## 1A high none 5
## 2A high optX10
## 3A 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 none10
## 12 A med optX 2
## 13 A med optZ 5
## 14 med none15
## 15 med optZ 2
## 16 A low none 7
## 17 A low optX 7
## 18 B low none10
## 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 -
