Re: [R-pkg-devel] re-exporting plot method?
Hi Simon,
Thanks for the detailed answer. I had considered all those
possibilities, and was hoping that I had just missed something obvious.
I have been using S4 classes in my own packages for quite a while. But
here, I didn't see any need to create my own class. Now, I may make my
own, which presents a more abstract "graph" that can have realizations
both as 'igraph' or "graphNEL' - 'Rargaph'. I'll have to think about,
but that seems like the only reliable way to prevent putting al of
Rgraphviz into the user's namespace.
Oh, and CRAN doesn't complain about importing Rgraphviz, since
BioConductor is one of the "standard mainstream" repositories.
Best,
Kevin
On 4/30/2024 11:46 PM, Simon Urbanek wrote:
Kevin,
welcome to the S4 world! ;) There is really no good solution since S4 only
works at all if you attach the package since it relies on replacing the base S3
generic with its own - so the question remains what are your options to do it.
The most obvious is to simply add Depends: Rgraphviz which makes sure that any
generics required are attached so your package doesn't need to worry. This is
the most reliable in a way as you are not limiting the functionality to methods
you know about. The side-effect, though, (beside exposing functions the user
may not care about) is that such package cannot be on CRAN since Rgraphics is
not on CRAN (that said, you mentioned you are already importing then you seem
not to worry about that).
The next option is to simply ignore Rgraphviz and instead add setGeneric("plot") to your
package and add methods to Depends and importFrom(methods, setGeneric) + exportMethods(plot) to the
namespace. This allows you to forget about any dependencies - you are just creating the S4 generic
from base::plot to make the dispatch work. This is the most light-weight solution as you only
cherry-pick methods you need and there are no dependencies other than "methods". However,
it is limited to just the functions you care about.
Finally, you could re-export the S4 plot generic from Rgraphviz, but I'd say
that is the least sensible option, since it doesn't have any benefit over doing
it yourself and only adds a hard dependency for no good reason. Also copying
functions from another package opens up a can of worms with versions etc. -
even if the risk is likely minimal.
Just for completeness - a really sneaky way would be to export an S3 plot method from
your package - it would be only called in the case where the plot generic has not been
replaced yet, so you could "fix" things on the fly by calling the generic from
Rgraphviz, but that sounds a little hacky even for my taste ;).
Cheers,
Simon
On 1/05/2024, at 6:03 AM, Kevin R. Coombes wrote:
Hi,
I am working on a new package that primarily makes use of "igraph" representations of certain mathematical graphs, in
order to apply lots of the comp sci algorithms already implemented in that package. For display purposes, my "igraph"
objects already include information that defines node shapes and colors and edge styles and colors. But, I believe that the
"graph" - "Rgraphviz" - "graphNEL" set of tools will produce better plots of the graphs.
So, I wrote my own "as.graphNEL" function that converts the "igraph" objects I want to
use into graphNEL (or maybe into "Ragraph") format in order to be able to use their graph layout
and rendering routines. This function is smart enough to translate the node and edge attributes from igraph
into something that works correctly when plotted using the tools in Rgraphviz. (My DESCRIPTION and NAMESPACE
files already import the set of functions from Rgraphviz necessary to make this happen.)
In principle, I'd like the eventual user to simply do something like
library("KevinsNewPackage")
IG <- makeIgraphFromFile(sourcefile)
GN <- as.graphNEL(IG)
plot(GN)
The first three lines work fine, but the "plot" function only works if the user
also explicitly includes the line
library("Rgraphviz")
I suspect that there is a way with imports and exports in the NAMESPACE to make
this work without having to remind the user to load the other package. But (in
part because the plot function in Rgraphviz is actually an S4 method, which I
don't need to alter in any way), I'm not sure exactly what needs to be imported
or exported.
Helpful suggestion would be greatly appreciated.
Best,
Kevin
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] re-exporting plot method?
Kevin,
welcome to the S4 world! ;) There is really no good solution since S4 only
works at all if you attach the package since it relies on replacing the base S3
generic with its own - so the question remains what are your options to do it.
The most obvious is to simply add Depends: Rgraphviz which makes sure that any
generics required are attached so your package doesn't need to worry. This is
the most reliable in a way as you are not limiting the functionality to methods
you know about. The side-effect, though, (beside exposing functions the user
may not care about) is that such package cannot be on CRAN since Rgraphics is
not on CRAN (that said, you mentioned you are already importing then you seem
not to worry about that).
The next option is to simply ignore Rgraphviz and instead add
setGeneric("plot") to your package and add methods to Depends and
importFrom(methods, setGeneric) + exportMethods(plot) to the namespace. This
allows you to forget about any dependencies - you are just creating the S4
generic from base::plot to make the dispatch work. This is the most
light-weight solution as you only cherry-pick methods you need and there are no
dependencies other than "methods". However, it is limited to just the functions
you care about.
Finally, you could re-export the S4 plot generic from Rgraphviz, but I'd say
that is the least sensible option, since it doesn't have any benefit over doing
it yourself and only adds a hard dependency for no good reason. Also copying
functions from another package opens up a can of worms with versions etc. -
even if the risk is likely minimal.
Just for completeness - a really sneaky way would be to export an S3 plot
method from your package - it would be only called in the case where the plot
generic has not been replaced yet, so you could "fix" things on the fly by
calling the generic from Rgraphviz, but that sounds a little hacky even for my
taste ;).
Cheers,
Simon
> On 1/05/2024, at 6:03 AM, Kevin R. Coombes wrote:
>
> Hi,
>
> I am working on a new package that primarily makes use of "igraph"
> representations of certain mathematical graphs, in order to apply lots of the
> comp sci algorithms already implemented in that package. For display
> purposes, my "igraph" objects already include information that defines node
> shapes and colors and edge styles and colors. But, I believe that the "graph"
> - "Rgraphviz" - "graphNEL" set of tools will produce better plots of the
> graphs.
>
> So, I wrote my own "as.graphNEL" function that converts the "igraph" objects
> I want to use into graphNEL (or maybe into "Ragraph") format in order to be
> able to use their graph layout and rendering routines. This function is smart
> enough to translate the node and edge attributes from igraph into something
> that works correctly when plotted using the tools in Rgraphviz. (My
> DESCRIPTION and NAMESPACE files already import the set of functions from
> Rgraphviz necessary to make this happen.)
>
> In principle, I'd like the eventual user to simply do something like
>
> library("KevinsNewPackage")
> IG <- makeIgraphFromFile(sourcefile)
> GN <- as.graphNEL(IG)
> plot(GN)
>
> The first three lines work fine, but the "plot" function only works if the
> user also explicitly includes the line
>
> library("Rgraphviz")
>
> I suspect that there is a way with imports and exports in the NAMESPACE to
> make this work without having to remind the user to load the other package.
> But (in part because the plot function in Rgraphviz is actually an S4 method,
> which I don't need to alter in any way), I'm not sure exactly what needs to
> be imported or exported.
>
> Helpful suggestion would be greatly appreciated.
>
> Best,
> Kevin
>
> __
> R-package-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
[R-pkg-devel] re-exporting plot method?
Hi,
I am working on a new package that primarily makes use of "igraph"
representations of certain mathematical graphs, in order to apply lots
of the comp sci algorithms already implemented in that package. For
display purposes, my "igraph" objects already include information that
defines node shapes and colors and edge styles and colors. But, I
believe that the "graph" - "Rgraphviz" - "graphNEL" set of tools will
produce better plots of the graphs.
So, I wrote my own "as.graphNEL" function that converts the "igraph"
objects I want to use into graphNEL (or maybe into "Ragraph") format in
order to be able to use their graph layout and rendering routines. This
function is smart enough to translate the node and edge attributes from
igraph into something that works correctly when plotted using the tools
in Rgraphviz. (My DESCRIPTION and NAMESPACE files already import the set
of functions from Rgraphviz necessary to make this happen.)
In principle, I'd like the eventual user to simply do something like
library("KevinsNewPackage")
IG <- makeIgraphFromFile(sourcefile)
GN <- as.graphNEL(IG)
plot(GN)
The first three lines work fine, but the "plot" function only works if
the user also explicitly includes the line
library("Rgraphviz")
I suspect that there is a way with imports and exports in the NAMESPACE
to make this work without having to remind the user to load the other
package. But (in part because the plot function in Rgraphviz is actually
an S4 method, which I don't need to alter in any way), I'm not sure
exactly what needs to be imported or exported.
Helpful suggestion would be greatly appreciated.
Best,
Kevin
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
