RAMIGO gives an error when displaying GO terms
1
1
Entering edit mode
7.5 years ago
biotech ▴ 560

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 <a href="http://amigo.geneontology.org/visualize">here</a>.
</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 • 2.5k views
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0
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Perhaps you could get better help if you told us what errors you are getting and the code you used that produce those errors?

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0
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That's a good idea, R code has been added to the question.

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0
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It is giving you an error where it is saying "unable to open <!DOCTYPE...". Seems like you might have switched some things around.

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0
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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.

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2
Entering edit mode
7.5 years ago

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. 

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Entering edit mode

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

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