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reshaping of data for barplot2

8 messages · Jean-Louis Abitbol, Marc Schwartz, Peter Dalgaard +3 more

Original
Jean-Louis Abitbol
# 
Dear All,

I have  the following data coming out from 

s <- with(final,
           summarize(norm, llist(gtt,fdiab),
                     function(norm) {
                      n <- sum(!is.na(norm))
                      s <- sum(norm, na.rm=T)
                      binconf(s, n)
                     }, type='matrix')
)
ie 

     gtt fdiab   norm.norm  norm.norm2  norm.norm3
18    PL    No  3.70370370  0.18997516 18.28346593
19    PL   Yes  3.57142857  0.18319034 17.71219774
13    TT1   No  9.09090909  3.59221932 21.15923917
14    TT1  Yes  1.81818182  0.09326054  9.60577606
...
10  HIGH    No 26.53061224 16.21128213 40.26228897
11  HIGH   Yes 10.00000000  4.66428345 20.14946472

I would like to reshape the data so that I can barplot2 treatments (gtt)
with 2 beside bars for fdiab  yes/no and add CI.

Various attemps have been unsuccessful as I have not understood both the
logic of beside and the nature of structures to be passed to barplot2.
Not enough know-how with reshape and transpose either.

Needless to say Dotplot works great with this kind of data but some
"Authority" requests side:side bars with CI.

Thanks for any help.

JL
Marc Schwartz
#
On Wed, 2004-11-24 at 19:24 +0100, Jean-Louis Abitbol wrote:
Jean-Louis,

For an easy example, see the help in barplot2, which uses the VADeaths
dataset. The dataset looks like:
Rural Male Rural Female Urban Male Urban Female
50-54       11.7          8.7       15.4          8.4
55-59       18.1         11.7       24.3         13.6
60-64       26.9         20.3       37.0         19.3
65-69       41.0         30.9       54.6         35.1
70-74       66.0         54.3       71.1         50.0

Now use:

barplot2(VADeaths)

This will yield a stacked bar plot, where there are 4 bars (one for each
column in the matrix). Each bar then consists of 5 stacked sections,
with each section representing the row values in each column.

Now try:

barplot(VADeaths, beside = TRUE)

This now yields 4 groups of bars, with one group for each column. Each
group then consists of 5 bars, one bar for each row value.

Hopefully, that gives you some insight into how the matrix structure
interacts with the 'beside' argument.

In the case of your data above, I read the few rows into a data frame
called 'df'. So 'df' looks like:
gtt fdiab norm.norm  norm.norm2 norm.norm3
1   PL    No  3.703704  0.18997516  18.283466
2   PL   Yes  3.571429  0.18319034  17.712198
3  TT1    No  9.090909  3.59221932  21.159239
4  TT1   Yes  1.818182  0.09326054   9.605776
5 HIGH    No 26.530612 16.21128213  40.262289
6 HIGH   Yes 10.000000  4.66428345  20.149465


To follow the VADeaths example above, you need to re-shape the required
columns, each as three column matrices, as follows:

height <- matrix(df$norm.norm, ncol = 3)
ci.l <- matrix(df$norm.norm2, ncol = 3)
ci.u <- matrix(df$norm.norm3, ncol = 3)
bars <- matrix(df$fdiab, ncol = 3)

Now, 'height' looks like:
[,1]     [,2]     [,3]
[1,] 3.703704 9.090909 26.53061
[2,] 3.571429 1.818182 10.00000

ci.l and ci.u and bars will of course look similar.


So, now you could use barplot2 as follows:

mp <- barplot2(height, plot.ci = TRUE, 
               ci.l = ci.l, ci.u = ci.u, beside = TRUE,
               names.arg = bars)


Note that I save the bar midpoints in 'mp'.

Now, you can go back and put in the bar group labels as follows. First
break out the unique values of 'gtt' keeping the order intact by using
matrix():

labels <- matrix(df$gtt, ncol = 2, byrow = TRUE)
mtext(side = 1, at = colMeans(mp), text = labels[, 1], line = 3)

Note that I use 'byrow = TRUE' in the call to matrix() so that the order
of the matrix is set properly. Thus, each column contains the group
labels and looks like:
[,1]   [,2]  
[1,] "PL"   "PL"  
[2,] "TT1"  "TT1" 
[3,] "HIGH" "HIGH"

So we just use the first column above in the call to mtext().


So that should do it and can be extended to your full dataset if the
format is consistent with what you have above.


One final (and important) note.  There is another approach here that can
be used, which is to keep your data in its initial state and specify the
'space' argument explicitly in the call to barplot2. This is actually
less work than what we did above. In this case, we use the 'space'
argument to group the bars explicitly, which is in effect, what the
'beside' argument does internally.

We use each column from 'df' directly and set the 'space' argument to a
repeating sequence of c(1, 0) for each of the 3 groups. Note that here
we need to explicitly define the colors to use, since barplot2 uses
'grey' by default when 'height' is a vector (as does barplot). We also
need to convert df$diab to a vector, otherwise the numeric factor codes
will be used.

The sequence then goes like this:

mp <- barplot2(df$norm.norm, plot.ci = TRUE, 
               ci.l = df$norm.norm2, ci.u = df$norm.norm3,
               space = rep(c(1, 0), 3),
               col = rep(c("red", "yellow"), 3),
               names.arg = as.vector(df$fdiab))

Now, as before, we create the 'labels' matrix.

labels <- matrix(df$gtt, ncol = 2, byrow = TRUE)

Now, use mtext() for the group. Note that since 'height' was a vector
and not a matrix, 'mp' will be as well. Thus, we need to convert the
'mp' vector to a matrix to get the group midpoints:

mtext(side = 1, at = colMeans(matrix(mp, ncol = 3)), 
      text = labels[, 1], line = 3)


Which approach you take is up to you. As you see, either one will work.

HTH,

Marc Schwartz
<Will be away from e-mail for a while. Will check back later>
Robert Baer
# 
I went through the following steps using RGUI menus to install gregmisc from
CRAN.  It appears to install but at the end R does not seem to be able to
find it.  Any idea what I'm doing wrong?

Thankjs,
Rob
----------------------------
+ install.packages(select.list(a[,1],,TRUE), .libPaths()[1], available=a,
dependencies=TRUE)})
trying URL `http://cran.r-project.org/bin/windows/contrib/2.0/PACKAGES'
Content type `text/plain; charset=iso-8859-1' length 23113 bytes
opened URL
downloaded 22Kb

trying URL
`http://cran.r-project.org/bin/windows/contrib/2.0/gregmisc_2.0.0.zip'
Content type `application/zip' length 687958 bytes
opened URL
downloaded 671Kb

bundle 'gregmisc' successfully unpacked and MD5 sums checked

Delete downloaded files (y/N)? y

updating HTML package descriptions
Error in library(gregmisc) : There is no package called 'gregmisc'
_
platform i386-pc-mingw32
arch     i386
os       mingw32
system   i386, mingw32
status
major    2
minor    0.1
year     2004
month    11
day      15
language R
Peter Dalgaard
# 
"Robert W. Baer, Ph.D." <rbaer at atsu.edu> writes:
It's a bundle nowadays, so you need to load one of it's constituent
packages.
Brian Ripley
# 
gregmisc is a bundle, not a package.  Its description on CRAN is

gregmisc	Bundle of gtools, gdata, gmodels, gplots

so try one of those packages.
On Wed, 24 Nov 2004, Robert W. Baer, Ph.D. wrote:

            

      
      
      
    

        
^^^^^^^

            

      
      
      
    

        
^^^^^^^

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Robert Baer
    

    

      
      #
    

  


  

      
Thanks for the clarification.

Pursuant to the recent dicussion of GUI promoting ignornce among users, I
plead guilty for CRAN installs  but they have generally saved so much
time.<g>.  This does raise the question as to whether gregmisc and other
bundles should appear on the "install packages from CRAN" pop-up in RGUI.
It also leaves me wondering what exactly was the REAL result of the
apparently successful  gregmisc install .

I did help.search("bundle") and coming away with nada.  I am not sure where
I should head to de-dumb myself.  I found a little in writing R extensions,
but this did not clarify the interaction with the RGUI install procedure for
me.

Thanks again.

Rob

-----------------------------------------
----- Original Message ----- 
From: "Peter Dalgaard" <p.dalgaard at biostat.ku.dk>
To: "Robert W. Baer, Ph.D." <rbaer at atsu.edu>
Cc: "R-Help" <r-help at stat.math.ethz.ch>
Sent: Wednesday, November 24, 2004 4:13 PM
Subject: Re: [R] Installing gregmisc under windows 2000

            

      
      
      
    

        
from

            

      
      
      
    

        
to

            

      
      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Yuandan Zhang
    

    

      
      #
    

  


  

      
That seems not the case under linux in term of installation. You can install this bundle in the same way as installing an individul package.

eg 

R CMD INSTALL  CRAN/contrib/main/gregmisc_2.0.0.tar.gz

to get all constituent packages installed. 
 
 
On Wed, 24 Nov 2004 22:14:14 +0000 (GMT)

        
Prof Brian Ripley <ripley at stats.ox.ac.uk> wrote:

        

            

      
      
      
    

        

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Brian Ripley
    

    

      
      #
    

  


  

      
On Thu, 25 Nov 2004, Yuandan Zhang wrote:

        

            

      
      
      
    

        
And the same under Windows.  Please read the rest of the message you 
silently excised.

As gregmisc is not one of the constituent packages, library(gregmisc) does 
not work under Linux.

What exactly were you trying to `correct'?

            

      
      
      
    

        
[Important details removed here.]