S-Plus Trellis Graphs: Reading and Annotating p-values to trellis Plots

[Ya-Lin Chiu <ychiu@scharp.org>]

Hi, To whom it may concern:

    I'm a statistician in Seattle. My co-worker send me the following message, 
and we are trying to put "p-value" for each factorA*factorB in xyplot. The goal 
is not to hard coded p-value, but input as a dataset. The following code seems 
not working for me. My understanding from these codes is either hard coded and 
inner function of render.trellis.
    
    I'm wondering if there's anyone doing such task before and can share w/ me. 
Thanks.
    
Best,

Ya-lin
------------- Begin Forwarded Message -------------

From: John Payne <jcpayne@u.washington.edu>
To: s-news@lists.biostat.wustl.edu
Subject: [S] Summary: Text for individual panels in a trellis plot
Date: Thu, 29 May 2003 00:14:32 -0700
Sender: s-news-owner@lists.biostat.wustl.edu
X-Mailer: Microsoft Outlook Express 6.00.2800.1106

Many thanks for the swift, thoughtful and extremely helpful replies I received 
from the members of this community.  In brief, I asked how to label individual 
panels in a trellis plot of the form 
xyplot(y~x|factorA*factorB, groups = factorC) when some of the factor 
combinations are missing.  Bert Gunter and Henrik Aalborg Nielsen suggested 
inserting an 'if' statement into the panel function, such as this:

.... panel=function(x,y,...){
if(length(y) == 0){ ## or whatever test you want
text(..., label= 'Insufficient Data',cex=2)
}
else panel.xyplot(x,y,...) ## or whatever plotting code you like

However, in my case the problem is that the panel function is not invoked if 
there are no data.  Jim Pratt pointed out that you can determine which panel 
you 
are working on by
    pnl<-get('n',frame=sys.parent())
and in the same vein, Bill Dunlap showed me how to label each panel with its
row, column and number:

a <- data.frame(g1 = rep(letters[1:2], each = 18), g2 = rep(LETTERS[6:8],each = 
12), 
    y = sort(rnorm(36)),x = sort(runif(36)))
xyplot(y ~ x | g2 * g1, data = a,
          panel = function(...){
                panel.xyplot(...);
                mtext(side=1,line=-2,text=paste(n=eval(Quote(paste("n=", 
n,"p=",p,"q=",q)),local=sys.parent())))
          })
However, he warns that n, p and q "are variables in the function 
render.trellis(), which is the function
that actually calls the panel function.  It is a messy way of doing things and 
I 
would rather have things depend what is given to panel, like length(x) or the 
subscripts argument (it tells you which rows in the data frame are
being passed to the panel function), but sometimes the panel number is what you 
need.  If the function render.trellis ever got rewritten you wouldn't be able 
to 
depend on n, p, and q still being used."

Finally Nick Ellis suggested a very clever solution, which I give in full.  He 
wrote:

I can't see a simple way of doing it because the panel function doesn't get
invoked if there's no data:

df <- expand.grid(a=letters[1:3],b=LETTERS[1:3],x=1:10)
df$z <- df$x+rnorm(df$x)
sub <- df$a=="b" & df$b=="B"
xyplot(z~x|a*b,df[!sub,],panel=function(...){
panel.xyplot(...)
text(mean(par("usr")[1:2]),mean(par("usr")[3:4]),"hello")
})

Here is a fairly kludgy way to do it by putting dummy data into every factor
combination, then only plotting the real data or a text message:

dummy 
<-cbind(expand.grid(a=levels(df$a),b=levels(df$b)),x=mean(df$x),z=mean(df$z))
xyplot(z~x|a*b,rbind(dummy,df[!sub,]),panel=function(x,y,...){
if(length(x)==1)
text(mean(par("usr")[1:2]),mean(par("usr")[3:4]),"No data")
else panel.xyplot(x[-1],y[-1],...)
})

If I understand it correctly, the point of making the dummy values the means of 
x and y is to ensure that the dummy values don't influence the calculation of 
the x and y plotting limits.  

Thanks so much to everyone for your help!

John Payne
Box 351800
Dept. of Zoology
University of Washington
Seattle, WA 98195


=====================================================================
Mark Deers, M.A.
Statistical Research Associate

SCHARP (Statistical Center for HIV/AIDS Research and Prevention)
Fred Hutchinson Cancer Research Center
1100 Fairview Ave N, MW-500
PO Box 19024
Seattle, WA 98109-1024

Phone:  206-667-6887 
Fax:    206-667-4812
e-mail: mark@scharp.org
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- ------------- End Forwarded Message -------------


=====================================================================
YA-LIN CHIU, M.S.
Statistical Research Associate
Fred Hutchinson Cancer Research Center
SCHARP (Statistical Center for HIV/AIDS Research and Prevention)
Phone:  (206)667-6176 
Fax:    (206)667-4812
e-mail: ychiu@scharp.org

CONFIDENTIALITY NOTICE: This e-mail message and any attachments may be 
confidential and privileged. If you are not intended to receive this message, 
please notify the sender and destroy the message. Thank you.

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