R help - Jun 2015 - R lattice : labeling of matrix groups of different size with strips

Hi Duncan,


thank you very much for your help.


Originally, I thought that it is possible to use a different data
representation and then to automatically create the plots and strips
in lattice.

Based on your suggestion, I could write the code for an annotated
levelplot of the two groups (code is shown below).

An open question is how to display the two groups with the same aspect
ratio for the rows.

> plotMatrix
> , , group1
>
>   a b c d
> 1 1 0 0 0
> 2 1 0 0 0
> 3 1 1 0 0
> 4 0 1 0 0
> 5 0 1 1 0
>
> , , group2
>
>    a  b  c  d
> 1  0  0  1  0
> 2  0  0  1  1
> 3  0  0  0  1
> 4 NA NA NA NA
> 5 NA NA NA NA
library(gridExtra)

trellis.device(device = "pdf",file
="lattice_annotated_groups.pdf",width=8,height=5)

#The aspect="fill" option was added to coerce the same height of the 2
plots
#panel.text was used instead of grid.text to avoid using the
latticeExtra package

plot1 <- levelplot(plotMatrix[,,1],
             page = function(n)
             panel.text("group 1",
                 x = 0.5,
                 y = 0.96),
             colorkey = F,
             xlab = "",
             ylab="",
             aspect="fill")

pm <- plotMatrix[1:3,,2]
colnames(pm) <- rep("",ncol(pm))

plot2 <-levelplot(pm,
            page = function(n)
            panel.text(
                "group 2",
                 x = 0.5,
                 y = 0.96),
            colorkey = F,
            xlab = "",
            ylab="",
            aspect="fill")


grid.arrange(plot1,plot2,ncol=2)
dev.off()
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I am not sure that changing the aspect ratio by using 
levelplot(plotMatrix[,,2],
                 aspect = 1/0.6,
                 ...)

will do the job as I seem to remember doing something like that when first
looking at your problem. There were unwanted side effects

using grid.arrange is the quick way to fill the plot area, I rarely use it

You may be better off by using print - I have not got your original data so I
can only guess
eg

print(plot2, position = c(0.2,0,0.8,0.5), more = TRUE)
print(plot1 position = c(0,0.5,1.1), more = FALSE)

You may have to fiddle with the position values for plot2 to get it right.

If the text of plot2 is too small then you could put a line in to get plot2
par.settings = list(fontsize = list(text = 12.5, points = 8)),  
this is device dependent and you may need to change it

 Regards

Duncan


-----Original Message-----
From: R-help [mailto:r-help-bounces at r-project.org] On Behalf Of R codeplayer
Sent: Thursday, 25 June 2015 21:01
To: r-help at r-project.org
Subject: Re: [R] R lattice : labeling of matrix groups of different size with
strips

Hi Duncan,


thank you very much for your help.


Originally, I thought that it is possible to use a different data
representation and then to automatically create the plots and strips
in lattice.

Based on your suggestion, I could write the code for an annotated
levelplot of the two groups (code is shown below).

An open question is how to display the two groups with the same aspect
ratio for the rows.

> plotMatrix
> , , group1
>
>   a b c d
> 1 1 0 0 0
> 2 1 0 0 0
> 3 1 1 0 0
> 4 0 1 0 0
> 5 0 1 1 0
>
> , , group2
>
>    a  b  c  d
> 1  0  0  1  0
> 2  0  0  1  1
> 3  0  0  0  1
> 4 NA NA NA NA
> 5 NA NA NA NA
library(gridExtra)

trellis.device(device = "pdf",file
="lattice_annotated_groups.pdf",width=8,height=5)

#The aspect="fill" option was added to coerce the same height of the 2
plots
#panel.text was used instead of grid.text to avoid using the
latticeExtra package

plot1 <- levelplot(plotMatrix[,,1],
             page = function(n)
             panel.text("group 1",
                 x = 0.5,
                 y = 0.96),
             colorkey = F,
             xlab = "",
             ylab="",
             aspect="fill")

pm <- plotMatrix[1:3,,2]
colnames(pm) <- rep("",ncol(pm))

plot2 <-levelplot(pm,
            page = function(n)
            panel.text(
                "group 2",
                 x = 0.5,
                 y = 0.96),
            colorkey = F,
            xlab = "",
            ylab="",
            aspect="fill")


grid.arrange(plot1,plot2,ncol=2)
dev.off()

Hi Duncan,


thank you so much for your help.


2015-06-26 4:16 GMT+02:00 Duncan Mackay <dulcalma at
bigpond.com>:
> I am not sure that changing the aspect ratio by using
> levelplot(plotMatrix[,,2],
>                  aspect = 1/0.6,
>                  ...)
I already experimented with different values of aspect but I newer get
the height of the groups to match

>
> will do the job as I seem to remember doing something like that when first
looking at your problem. There were unwanted side effects
>
> using grid.arrange is the quick way to fill the plot area, I rarely use it
>
> You may be better off by using print - I have not got your original data so
I can only guess
> eg
>
> print(plot2, position = c(0.2,0,0.8,0.5), more = TRUE)
> print(plot1 position = c(0,0.5,1.1), more = FALSE)
In this approach, I get a different size for the height and width of the groups.
> You may have to fiddle with the position values for plot2 to get it right.
>
> If the text of plot2 is too small then you could put a line in to get plot2
> par.settings = list(fontsize = list(text = 12.5, points = 8)),
> this is device dependent and you may need to change it
>
>  Regards
>
> Duncan
>
Thank you for your time
> -----Original Message-----
> From: R-help [mailto:r-help-bounces at r-project.org] On Behalf Of R
codeplayer
> Sent: Thursday, 25 June 2015 21:01
> To: r-help at r-project.org
> Subject: Re: [R] R lattice : labeling of matrix groups of different size
with strips
>
> Hi Duncan,
>
>
> thank you very much for your help.
>
>
> Originally, I thought that it is possible to use a different data
> representation and then to automatically create the plots and strips
> in lattice.
>
> Based on your suggestion, I could write the code for an annotated
> levelplot of the two groups (code is shown below).
>
> An open question is how to display the two groups with the same aspect
> ratio for the rows.
>
>
>> plotMatrix
>> , , group1
>>
>>   a b c d
>> 1 1 0 0 0
>> 2 1 0 0 0
>> 3 1 1 0 0
>> 4 0 1 0 0
>> 5 0 1 1 0
>>
>> , , group2
>>
>>    a  b  c  d
>> 1  0  0  1  0
>> 2  0  0  1  1
>> 3  0  0  0  1
>> 4 NA NA NA NA
>> 5 NA NA NA NA
>
> library(gridExtra)
>
> trellis.device(device = "pdf",file
> ="lattice_annotated_groups.pdf",width=8,height=5)
>
> #The aspect="fill" option was added to coerce the same height of
the 2 plots
> #panel.text was used instead of grid.text to avoid using the
> latticeExtra package
>
> plot1 <- levelplot(plotMatrix[,,1],
>              page = function(n)
>              panel.text("group 1",
>                  x = 0.5,
>                  y = 0.96),
>              colorkey = F,
>              xlab = "",
>              ylab="",
>              aspect="fill")
>
> pm <- plotMatrix[1:3,,2]
> colnames(pm) <- rep("",ncol(pm))
>
> plot2 <-levelplot(pm,
>             page = function(n)
>             panel.text(
>                 "group 2",
>                  x = 0.5,
>                  y = 0.96),
>             colorkey = F,
>             xlab = "",
>             ylab="",
>             aspect="fill")
>
>
> grid.arrange(plot1,plot2,ncol=2)
> dev.off()
>
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