Question: RAMIGO gives an error when displaying GO terms
1
gravatar for biotech
4.6 years ago by
biotech540
United States
biotech540 wrote:

 

I have a list of enriched GO terms and would like to have something like the following graph. This graph was done using RAMIGO R package, but now is giving me errors.

Thanks

Here is the RAMIGO error:

> library(RamiGO)

Loading required package: gsubfn

Loading required package: proto

> d = read.table("same_GOs.txt", header = TRUE) # note that required a header named 'GOs'

> v <- as.vector(d$GOs)

> color <- c("lightblue")

> #v <- as.vector(d$GOs)

> goIDs <- v

> pngRes <- getAmigoTree(goIDs=goIDs, color=color, filename="example", picType="png", saveResult=TRUE)

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>

The document has moved http://amigo.geneontology.org/visualize">here.

</body></html>

> sessionInfo()

R version 3.0.3 (2014-03-06)

Platform: x86_64-apple-darwin10.8.0 (64-bit)

 

locale:

[1] C/UTF-8/C/C/C/C

 

attached base packages:

[1] stats     graphics  grDevices utils     datasets  methods   base     

 

other attached packages:

[1] RamiGO_1.8.1 gsubfn_0.6-6 proto_0.3-10

 

loaded via a namespace (and not attached):

 [1] BiocGenerics_0.8.0 RCurl_1.95-4.5     RCytoscape_1.12.0  XML_3.95-0.2      

 [5] XMLRPC_0.3-0       bitops_1.0-6       graph_1.40.1       igraph_0.7.1      

 [9] parallel_3.0.3     png_0.1-7          stats4_3.0.3       tcltk_3.0.3       

[13] tools_3.0.3

 

go • 1.8k views
ADD COMMENTlink modified 4.6 years ago by Michael Dondrup47k • written 4.6 years ago by biotech540

Perhaps you could get better help if you told us what errors you are getting and the code you used that produce those errors?

ADD REPLYlink written 4.6 years ago by Sean Davis25k

That's a good idea, R code has been added to the question.

ADD REPLYlink written 4.6 years ago by biotech540

It is giving you an error where it is saying "unable to open <!DOCTYPE...". Seems like you might have switched some things around.

ADD REPLYlink written 4.6 years ago by pld4.8k

I reinstalled the package yesterday. Similar error was reported previously: https://stat.ethz.ch/pipermail/bioconductor/2014-March/058337.html

but I'm not able to fix it as they suggest.

ADD REPLYlink written 4.6 years ago by biotech540
2
gravatar for Michael Dondrup
4.6 years ago by
Bergen, Norway
Michael Dondrup47k wrote:

This package seems to try to use the Amigo visualization web service at  

 http://amigo.geneontology.org/visualize to draw the graph but the endpoint was moved to  http://amigo.geneontology.org/amigo/visualize. You need to update R and the BioC package to the latest version, the version you have is very old, and then try again. 

ADD COMMENTlink modified 4.6 years ago • written 4.6 years ago by Michael Dondrup47k

Thanks Michael, your answer solved my question. RamiGO is working fine now.

ADD REPLYlink written 4.6 years ago by biotech540
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