Skip to content

ordering and plotting question

4 messages · Simon Melov, Stéphane Dray, Marc Schwartz +1 more

Simon Melov
# 
Hi,
I am trying to plot several rows out of a list of thousands. I have 40 
columns, and about 16,000 rows with the following Df structure.

ID X01 X02 X03..X40
AI456 45 64 23...
AI943 14 3 45 ..
AI278 78 12 68..
BW768 -2 -7 34..
...

My question is, I have a list of 100 IDs generated elsewhere 
(Df-"Ofinterest"), I would like to plot the 100 IDs from that data 
frame over the 40 columns (40 points per ID, with each column being 1 x 
value). But I cant figure out how to retrieve the values from the main 
Df and plot them. Ive tried looking at order, rank etc, but these seem 
to apply to numbers, and not text strings.

thanks

Simon.
Stéphane Dray
# 
Hello,

I would like to call C code from R. My C code is divided in two files. In 
the file "testpermut.c", I have the following lines:

#include "adesub.h"

In my working folder, I have the files:
- adesub.c which contains general functions
- adesub.h with the header of functions contained in adesub.c
- testpermut.c which call some functions defined in adesub.c

When I try to  create my dll (Work on Windows XP, R-1.8.1), I obtain error 
message:

$ Rcmd shlib testpermut.c
making adesub.d from adesub.c
making testpermut.d from testpermut.c
gcc   -Ic:/Rdev/R-1.8.1/src/include -Wall -O2   -c testpermut.c -o testpermut.o
ar cr testpermut.a *.o
ranlib testpermut.a
gcc  --shared -s  -o testpermut.dll testpermut.def 
testpermut.a  -Lc:/Rdev/R-1.8
.1/src/gnuwin32  -lg2c -lR
testpermut.a(testpermut.o.b)(.text+0x35):testpermut.c: undefined reference 
to `taballoc'
testpermut.a(testpermut.o.b)(.text+0x49):testpermut.c: undefined reference 
to `taballoc'
testpermut.a(testpermut.o.b)(.text+0x62):testpermut.c: undefined reference 
to `taballoc'
testpermut.a(testpermut.o.b)(.text+0x14c):testpermut.c: undefined reference 
to `freetab'
testpermut.a(testpermut.o.b)(.text+0x156):testpermut.c: undefined reference 
to `freetab'
testpermut.a(testpermut.o.b)(.text+0x160):testpermut.c: undefined reference 
to `freetab'
testpermut.a(testpermut.o.b)(.text+0x192):testpermut.c: undefined reference 
to `taballoc'
testpermut.a(testpermut.o.b)(.text+0x22b):testpermut.c: undefined reference 
to `taballoc'
testpermut.a(testpermut.o.b)(.text+0x23f):testpermut.c: undefined reference 
to `vecalloc'
testpermut.a(testpermut.o.b)(.text+0x24b):testpermut.c: undefined reference 
to `vecalloc'
testpermut.a(testpermut.o.b)(.text+0x339):testpermut.c: undefined reference 
to `freevec'
testpermut.a(testpermut.o.b)(.text+0x343):testpermut.c: undefined reference 
to `freevec'
testpermut.a(testpermut.o.b)(.text+0x34d):testpermut.c: undefined reference 
to `freetab'
testpermut.a(testpermut.o.b)(.text+0x412):testpermut.c: undefined reference 
to `taballoc'
make: *** [testpermut.dll] Error 1
$

The functions taballoc, freetab, vecalloc and freevec are defined in adesub 
files. So it seems that gcc does not make the links between my files. If I 
include the problematic functions in testpermut.c, gcc works perfectly and 
my dll is created.

Perhaps someone could explain me what is my problem although it is not an R 
problem but probably a misuse of gcc ?.

Thanks in advance.
St?phane DRAY
-------------------------------------------------------------------------------------------------- 

D?partement des Sciences Biologiques
Universit? de Montr?al, C.P. 6128, succursale centre-ville
Montr?al, Qu?bec H3C 3J7, Canada

Tel : 514 343 6111 poste 1233
E-mail : stephane.dray at umontreal.ca
-------------------------------------------------------------------------------------------------- 

Web                                          http://www.steph280.freesurf.fr/
Marc Schwartz
#
On Mon, 2004-02-02 at 14:13, Simon Melov wrote:
I am not entirely sure what type of plot you want, however the following
will enable you to subset the main dataframe, based upon matching ID's:

# Create an example vector of the ID's you want
df.index <- c("AI456", "AI278", "BW768")
[1] "AI456" "AI278" "BW768"
 
# Create a df with the subset of data you have above
df <- data.frame(ID = c("AI456", "AI943", "AI278", "BW768"),
                 X01 = c(45, 14, 78, -2),
                 X02 = c(64, 3, 12, -7),
                 X03 = c(23, 45, 68, 34))
ID X01 X02 X03
1 AI456  45  64  23
2 AI943  14   3  45
3 AI278  78  12  68
4 BW768  -2  -7  34

# Use which() and %in% to get a vector containing the
# row indices in df that match the three entries in df.index
found <- which(df$ID %in% df.index)
[1] 1 3 4

# Now subset df to include only those rows that match
MySubset <- df[found, ]
ID X01 X02 X03
1 AI456  45  64  23
3 AI278  78  12  68
4 BW768  -2  -7  34


MySubset now contains only those rows that match based upon your IDs in
the "index" vector.

If you know how to generate the plot you want from here, have at it. If
not, let me know what you wish to do and I can help further.

See ?which and ?%in% for more information. Also, see ?subset for
additional ways to subset dataframes using more complex logicals.

HTH,

Marc Schwartz
Brian Ripley
#
On Mon, 2 Feb 2004, Stephane DRAY wrote:

            

      
      
      
    

        
You only included one of the files. You need

Rcmd SHLIB testpermut.c adesub.c

I believe.