R help - Sep 2010 - Problems with "pdf" device using "plot" "glht" function on "multcomp" library.

Hi R users:

I have de following data frame (called "Sx")

  Descripcion         Nitratos
      Cont85g            72.40
      Cont85g           100.50
      Cont85g           138.30
      Cont80g           178.33
      Cont80g            79.01
      Cont80g            74.16
      Cont75g            23.70
      Cont75g            15.80
      Cont75g            16.20
    Patron80g            88.93
    Patron80g           113.01
    Patron80g            86.53

If I run this code without the "pdf" device
it works fine on the screen, but when I
use the "pdf" device it does not show in 
the "plot1.pdf" file what I got on the screen.

What am I doing wrong?

Thank you for your help.

library(multcomp)

Sx<-data.frame(Descripcion             
factor(c("Cont85g","Cont85g","Cont85g",
                      
"Cont80g","Cont80g","Cont80g",
                      
"Cont75g","Cont75g","Cont75g",
                      
"Patron80g","Patron80g","Patron80g")),
               Nitratos=c(72.40,100.50, 138.30,
                         178.33,79.01,74.16,
                         23.70, 15.80,16.20,
                         88.93,113.01,86.53))
pdf("plot1.pdf")
m1<-aov(Nitratos~Descripcion-1,data=Sx)
vect1<-table(Sx$Descripcion)
K<-contrMat(vect1,base=4)
dnk<-glht(m1,linfct=K)
summary(dnk)

old.par<-par(no.readonly = TRUE)
par(mai=c(1,2,1.25,1),mgp=c(3,1,0))
print(plot(dnk,las=1,xlab=""))
print(abline(v=0,lty=2))
par(old.par)

dev.off()

Thank you Jorge Iv?n:

Im working on a Linux platform, and with a recent pathed version of R.
Does it work on windows?


R version 2.11.1 Patched (2010-09-10 r52887)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=es_CO.UTF-8          LC_NUMERIC=C
LC_TIME=es_CO.UTF-8           LC_COLLATE=es_CO.UTF-8
LC_MONETARY=es_CO.UTF-8      
 [6] LC_MESSAGES=es_CO.UTF-8       LC_PAPER=es_CO.UTF-8
LC_NAME=es_CO.UTF-8           LC_ADDRESS=es_CO.UTF-8
LC_TELEPHONE=es_CO.UTF-8     
[11] LC_MEASUREMENT=es_CO.UTF-8    LC_IDENTIFICATION=es_CO.UTF-8

attached base packages:
[1] splines   stats     graphics  grDevices utils     datasets  methods
base     

other attached packages:
[1] multcomp_1.2-0     survival_2.35-8    mvtnorm_0.9-92
RColorBrewer_1.0-2 lattice_0.19-11    rkward_0.5.3      

loaded via a namespace (and not attached):
[1] grid_2.11.1  tools_2.11.1


El mar, 14-09-2010 a las 12:37 -0400, Jorge Ivan Velez
escribi?:
> Hola Kenneth,
> 
> 
> Acabo de correrlo en un Mac y funciona bien. Cual es tu sessionInfo()?
> 
> 
> Saludos,
> Jorge
> 
> 
> > sessionInfo()
> R version 2.11.1 Patched (2010-05-31 r52180) 
> x86_64-apple-darwin9.8.0 
> 
> 
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
> 
> 
> attached base packages:
> [1] splines   stats     graphics  grDevices utils     datasets
>  methods   base     
> 
> 
> other attached packages:
> [1] multcomp_1.2-0  survival_2.35-8 mvtnorm_0.9-92  seqinr_3.0-0
>  MuMIn_0.13.14  
> 
> 
> loaded via a namespace (and not attached):
> [1] tools_2.11.1
> 
> 
> 
> 
> On Tue, Sep 14, 2010 at 12:34 PM, Kenneth Roy Cabrera Torres
> <krcabrer at une.net.co> wrote:
>         Hi R users:
>         
>         I have de following data frame (called "Sx")
>         
>          Descripcion         Nitratos
>              Cont85g            72.40
>              Cont85g           100.50
>              Cont85g           138.30
>              Cont80g           178.33
>              Cont80g            79.01
>              Cont80g            74.16
>              Cont75g            23.70
>              Cont75g            15.80
>              Cont75g            16.20
>            Patron80g            88.93
>            Patron80g           113.01
>            Patron80g            86.53
>         
>         If I run this code without the "pdf" device
>         it works fine on the screen, but when I
>         use the "pdf" device it does not show in
>         the "plot1.pdf" file what I got on the screen.
>         
>         What am I doing wrong?
>         
>         Thank you for your help.
>         
>         library(multcomp)
>         
>         Sx<-data.frame(Descripcion>                     
factor(c("Cont85g","Cont85g","Cont85g",
>                              
"Cont80g","Cont80g","Cont80g",
>                              
"Cont75g","Cont75g","Cont75g",
>                              
"Patron80g","Patron80g","Patron80g")),
>                       Nitratos=c(72.40,100.50, 138.30,
>                                 178.33,79.01,74.16,
>                                 23.70, 15.80,16.20,
>                                 88.93,113.01,86.53))
>         pdf("plot1.pdf")
>         m1<-aov(Nitratos~Descripcion-1,data=Sx)
>         vect1<-table(Sx$Descripcion)
>         K<-contrMat(vect1,base=4)
>         dnk<-glht(m1,linfct=K)
>         summary(dnk)
>         
>         old.par<-par(no.readonly = TRUE)
>         par(mai=c(1,2,1.25,1),mgp=c(3,1,0))
>         print(plot(dnk,las=1,xlab=""))
>         print(abline(v=0,lty=2))
>         par(old.par)
>         
>         dev.off()
>         
>         ______________________________________________
>         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.
> 
>

Hi R users:

I found a workaround for the problem I posted today.

I simple use "Cairo" library, then I use CairoPDF() function,
and it works!!!

The reason maybe is the acrobat reader, because the "okular" reader
from Ubuntu Linux shows the graphics just right.

Thank you for your help and advice.

Kenneth


El mar, 14-09-2010 a las 12:37 -0400, Jorge Ivan Velez
escribi?:
> Hola Kenneth,
> 
> 
> Acabo de correrlo en un Mac y funciona bien. Cual es tu sessionInfo()?
> 
> 
> Saludos,
> Jorge
> 
> 
> > sessionInfo()
> R version 2.11.1 Patched (2010-05-31 r52180) 
> x86_64-apple-darwin9.8.0 
> 
> 
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
> 
> 
> attached base packages:
> [1] splines   stats     graphics  grDevices utils     datasets
>  methods   base     
> 
> 
> other attached packages:
> [1] multcomp_1.2-0  survival_2.35-8 mvtnorm_0.9-92  seqinr_3.0-0
>  MuMIn_0.13.14  
> 
> 
> loaded via a namespace (and not attached):
> [1] tools_2.11.1
> 
> 
> 
> 
> On Tue, Sep 14, 2010 at 12:34 PM, Kenneth Roy Cabrera Torres
> <krcabrer at une.net.co> wrote:
>         Hi R users:
>         
>         I have de following data frame (called "Sx")
>         
>          Descripcion         Nitratos
>              Cont85g            72.40
>              Cont85g           100.50
>              Cont85g           138.30
>              Cont80g           178.33
>              Cont80g            79.01
>              Cont80g            74.16
>              Cont75g            23.70
>              Cont75g            15.80
>              Cont75g            16.20
>            Patron80g            88.93
>            Patron80g           113.01
>            Patron80g            86.53
>         
>         If I run this code without the "pdf" device
>         it works fine on the screen, but when I
>         use the "pdf" device it does not show in
>         the "plot1.pdf" file what I got on the screen.
>         
>         What am I doing wrong?
>         
>         Thank you for your help.
>         
>         library(multcomp)
>         
>         Sx<-data.frame(Descripcion>                     
factor(c("Cont85g","Cont85g","Cont85g",
>                              
"Cont80g","Cont80g","Cont80g",
>                              
"Cont75g","Cont75g","Cont75g",
>                              
"Patron80g","Patron80g","Patron80g")),
>                       Nitratos=c(72.40,100.50, 138.30,
>                                 178.33,79.01,74.16,
>                                 23.70, 15.80,16.20,
>                                 88.93,113.01,86.53))
>         pdf("plot1.pdf")
>         m1<-aov(Nitratos~Descripcion-1,data=Sx)
>         vect1<-table(Sx$Descripcion)
>         K<-contrMat(vect1,base=4)
>         dnk<-glht(m1,linfct=K)
>         summary(dnk)
>         
>         old.par<-par(no.readonly = TRUE)
>         par(mai=c(1,2,1.25,1),mgp=c(3,1,0))
>         print(plot(dnk,las=1,xlab=""))
>         print(abline(v=0,lty=2))
>         par(old.par)
>         
>         dev.off()
>         
>         ______________________________________________
>         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.
> 
>

Dear Ken,

it works for me on Linux. However, the print() commands around plot() are 
not necessary.

Torsten

Hi, Kenneth

It is not clear if you mean that your pdf output usually works, but it
does not in this special case, or that this is a first effort with
pdf.  The answer might depend on which is the case case.

If you are just getting started, can I refer you to some lecture notes
I made about saving graphs in R?

http://pj.freefaculty.org/R/SummerCamp2010/PJ-Lectures/plotting2.pdf

If you cut off the file name at the end,  you will see the list of the
other lectures I prepared for our university's "Summer Stats Camp"
in
2010.

If pdf does usually work, Could I suggest you take this code and
rearrange? Where you have this:

pdf("plot1.pdf")
m1<-aov(Nitratos~Descripcion-1,data=Sx)
vect1<-table(Sx$Descripcion)
K<-contrMat(vect1,base=4)
dnk<-glht(m1,linfct=K)
summary(dnk)

old.par<-par(no.readonly = TRUE)
par(mai=c(1,2,1.25,1),mgp=c(3,1,0))
print(plot(dnk,las=1,xlab=""))
print(abline(v=0,lty=2))
par(old.par)

dev.off()



Instead, separate the "stats" part from the plot part


m1 <- aov(Nitratos~Descripcion-1, data=Sx)
vect1 <- table(Sx$Descripcion)
K <- contrMat(vect1, base=4)
dnk <- glht(m1, linfct=K)
summary(dnk)

pdf("plot1.pdf", onefile=F, paper="special", height=6,
width=6)
### old.par<-par(no.readonly = TRUE)
par(mai = c(1, 2, 1.25, 1), mgp = c(3,1,0))
plot(dnk, las = 1, xlab = "")
abline(v = 0, lty = 2)
####par(old.par)
dev.off()

I've made changes to cut your "print" statements and moved your
pdf
command down to "sandwich" the plot commands.  I've added some
embellishment which I almost guarantee will make your pdf output more
useful.  (Spaces are inserted around <- and after commas for
readability.  Check the R examples, they generally recommend that).

To the R experts, it may be that the "par" stuff seems obvious, but to
the rest of us, well, it is not completely so.  You do not need to
save the par values because the par setting you change is instantly
forgotten when you do dev.off().   So you don't need to worry about
saving the default settings and then returning them.  Run par() to see
for yourself after dev.off().  par's defaults will be back where they
were at the beginning.

You would only need to do "remember my par" thing if you were trying
to put several graphs into a single output device, which you aren't.
And I've made that clear by putting onefile=F in the pdf statement.

I'd try it without the "par" at all if there is still trouble in
the
output file.

I added the paper="special" option in the pdf command in order to make
the margins in the output more reasonable. If you don't do that, the
pdf output assumes you are wanting a whole sheet of paper, so there
will be some massive margins in your output.

Good luck.

-- 
Paul E. Johnson
Professor, Political Science
1541 Lilac Lane, Room 504
University of Kansas