Hi, Prof Duncan
I am sorry to report to a wrong place. But I am lucky to meet you by
chance, right? Thanks first ^^
1. The variable y1 is an array get from Perl, each element is from a
database (the type should be numeric). Here is the code for that.
$query = qq{
select exonCount, count(hsEnsGene) as geneCount from countTop1000ks
group by exonCount order by exonCount;
};
$sql=$orthologDB->prepare($query);
$sql->execute()or die "Could not execute '$query' ...";
my @x1; my @y1;
while(my($exonCount, $geneCount) = $sql->fetchrow_array())
{
push(@x1, $exonCount);
push(@y1, $geneCount);
}
Here is the result if I print out the value in @y1:
print "y1---",join(" ",@y1), "---end\n";
% y1---101 44 33 26 8 15 18 13 3 5 4 2 1 4 1 1---end
But when I call
&R::callWithNames("barplot", {'',[EMAIL PROTECTED], 'main', 'Barplot
the Gene number per exon with top1000 low Ks', 'xlab', "Exon(low ks) number in
the gene",'ylab', 'Numbers of gene'});
It always says non-numeric argument:
% Error in -0.01 * height : non-numeric argument to binary operator
If I asign the value to another array, like
my @x=(101, 44, 33, 26, 8, 15, 18, 13, 3, 5, 4, 2, 1, 4, 1, 1);
&R::callWithNames("barplot", {'',[EMAIL PROTECTED], 'main', 'Barplot
the Gene number per exon with top1000 low Ks', 'xlab', "Exon(low ks) number in
the gene",'ylab', 'Numbers of gene'});
then it works.
I don't know why and what the difference is.
I also thought whether it is because of the different data type between
Perl and R, because in Perl, "3" and 3 could be same sometime. So I
call
&R::callWithNames("as.numeric",{'',[EMAIL PROTECTED]);
before I call
&R::callWithNames("barplot", {'',[EMAIL PROTECTED]);
Same error!
Same case if I change to use the R::boxplot([EMAIL PROTECTED]) as you said.
I am not sure I explain clear this time.
Looking forwards to your response!
Regards,
-Xianjun
On Thu, 2006-09-21 at 07:33 -0700, Duncan Temple Lang wrote:
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>
>
> Hi Xianjun
>
> [Important: Please don't send mail about an R package to r-bugs. That is
> for reporting bugs in R itself. Add on packages are different
> and it is only a coincidence that I am one of the R-core developers
> and package author. In general, all bug reports about
> a package should be sent to the author and questions should go to the
> author and the r-devel or r-help list as appropriate.]
>
>
> Is the problem you report a bug? Well not necessarily in RSPerl,
> but in your code. Unfortunately, you haven't told me what
> the variable y1 contains so it is hard to figure out what
> is going into the computations.
>
> A couple of things:
> a) Your example is calling boxplot in the first call and barplot
> in the second.
>
> b) in the first example, you are passing @y1 and in the second
> you are passing [EMAIL PROTECTED]
>
> I would guess that [EMAIL PROTECTED] is more appropriate and you might
> try that
> in the first case.
>
> c) the first case doesn't have any named arguments (just '') so why
> use callWithNames. Just R::boxplot([EMAIL PROTECTED])
>
>
> You are calling the R functions, but you are getting an error during
> the invocation. The error message is coming from R. So the
> problem is that you are passing inputs to the functions that it cannot
> handle. This can happen directly in R and so also in RSPerl. My guess
> is that you don't have the correct type of data in @y1 or that you are
> not passing it in the call as a reference.
>
> Xianjun Dong wrote:
> > Hi,
> >
> > It looks that not all function in R could be implemented by RSPerl. For
> > example, when I call
> >
> > &R::callWithNames("boxplot", {'',@y1});
> > or
> > R::barplot([EMAIL PROTECTED]);
> >
> > There would be error:
> >
> > Error in -0.01 * height : non-numeric argument to binary operator
> > Caught error in R::call()
> >
> > The same happened when calling "barplot", but it's ok to call plot.
> >
> > Is it a bug?
> >
>
> - --
> Duncan Temple Lang [EMAIL PROTECTED]
> Department of Statistics work: (530) 752-4782
> 4210 Mathematical Sciences Building fax: (530) 752-7099
> One Shields Ave.
> University of California at Davis
> Davis,
> CA 95616,
> USA
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