[BioC] Error in getAmigoTree (RamiGO package)

Fri Mar 14 22:04:06 CET 2014

Hi again,
I think I have found a work around by editing the source code.  In the file getAmigoTree.R, change the following:

Change line 1 from
getAmigoTree <- function(goIDs, color, pvalues, pcolors = c("white","tomato"), psplit = c(1,0.25,0.1,0.05,0.001), filename, picType = "png", modeType = "advanced", webserver, saveResult = TRUE)
to
getAmigoTree <- function(goIDs, color, pvalues, pcolors = c("white","tomato"), psplit = c(1,0.25,0.1,0.05,0.001), filename, picType = "png", modeType = "amigo", webserver, saveResult = TRUE)

Line 4 from
webserver <-"http://amigo.geneontology.org/cgi-bin/amigo/visualize"
to
webserver <-"http://amigo.geneontology.org/visualize"

Change line 37 from
if(modeType != "advanced"){
to
if(modeType != "amigo"){

-Suzy

-----Original Message-----
From: Dan Tenenbaum [mailto:dtenenba at fhcrc.org]
Sent: Friday, March 14, 2014 3:53 PM
To: Stiegelmeyer Suzy USRE
Cc: bioconductor at r-project.org; Markus Schroeder
Subject: Re: [BioC] Error in getAmigoTree (RamiGO package)

----- Original Message -----
> From: "suzy stiegelmeyer" <suzy.stiegelmeyer at syngenta.com>
> To: bioconductor at r-project.org
> Sent: Friday, March 14, 2014 12:48:55 PM
> Subject: [BioC] Error in getAmigoTree (RamiGO package)
>
> Hi everyone,
> I'm having some trouble with the RamiGO package.  I'm getting an error
> when executing getAmigoTree.  Can anyone recommend a workaround?
> Maybe the server is having a bad day but it is hard to tell.  Here is
> a log of what is happening:
>
> > ids=c("GO:0009058","GO:0015995")
> > pngamigo=getAmigoTree(goIDs=ids,color="pink",filename="test_bp.png",
> > picType="png",saveResult=T)
> Error in readPNG(aa) :
>   unable to open <!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML 2.0//EN">
> <html><head>
> <title>301 Moved Permanently</title>
> </head><body>
> <h1>Moved Permanently</h1>
> <p>The document has moved <a
> href="http://amigo.geneontology.org/visualize">here</a>.</p>
> </body></html>
>
> Looking in the code it has the default server as  webserver <-
> http://amigo.geneontology.org/cgi-bin/amigo/visualize.
> I tried a new webserver according to the "moved permanently message"
> above, but no luck.
> > pngamigo=getAmigoTree(goIDs=ids,color="pink",filename="grmzm2g323024
> > _bp.png",picType="png",webserver="http://amigo.geneontology.org/visu
> > alize",saveResult=T)
> Error: Internal Server Error
>

I think that not only has the URL moved, but the API of the web service has changed. So the Ramigo maintainer (CC'd) needs to fix the package. It's broken in both release and devel.

Dan

> So, any ideas?  Happy Friday BTW.
> Thanks,
> Suzy
>
> > sessionInfo()
> R version 3.0.3 (2014-03-06)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
>
> locale:
> [1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United
> States.1252
> [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C [5]
> LC_TIME=English_United States.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] RamiGO_1.8.0 gsubfn_0.6-5 proto_0.3-10 car_2.0-19
>
> loaded via a namespace (and not attached):
> [1] BiocGenerics_0.8.0 graph_1.40.1       igraph_0.7.0
>       MASS_7.3-30        nnet_7.3-7
>  [6] parallel_3.0.3     png_0.1-7          RCurl_1.95-4.1
>      RCytoscape_1.12.0  stats4_3.0.3
> [11] tcltk_3.0.3        tools_3.0.3        XML_3.98-1.1
>       XMLRPC_0.3-0
> _________________________________
>
> Suzy Stiegelmeyer, PhD
> Computational Biologist
> Bioinformatics
>
> Syngenta Biotechnology, Inc.
> 3054 Cornwallis Rd
> Research Triangle Park, NC
> 27709
> USA
>
> phone +1 919 281 7472
>
> suzy.stiegelmeyer at syngenta.com<mailto:suzy.stiegelmeyer at syngenta.com>
> www.syngenta.com<http://www.syngenta.com/>
>
>
>
>
> This message may contain confidential information. If
> yo...{{dropped:7}}
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>

This message may contain confidential information. If you are not the designated recipient, please notify the sender immediately, and delete the original and any copies. Any use of the message by you is prohibited. 