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Question: Shiny app for RefNet, PSICQUIC: annotated protein/protein interactions
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gravatar for pshannon
3.0 years ago by
pshannon80
United States
pshannon80 wrote:

In addressing some problems reported with using the RefNet package last week, I promised to follow up with an account of the RefNet/PSICQUIC shiny app.  

For background: the Bioc RefNet package  modestly extends the PSICQUIC package ("Proteomics Standards Initiative Query Interface").  Together they offer annotated interactions from many sources; RefNet adds some hand-curated interaction datasets stored in the AnnotationHub.    With very few exceptions, each of the > 150 million searchable interactions includes 

  1. Interaction type
  2. Detection method
  3. PubMed Id of article documenting the interaction
  4. Many alternate identifiers, with protein identifiers dominating

An IDMapper class provides HUGO gene symbols for most of the several kinds of protein identifiers returned by PSICQUIC.   RefNet currently adds a human metabolic network (recon2), stamlab TFs, and a 2006 angiogenesis-related hypoxia signaling network; these are intended as examples of the variety of interactions supported.  More additions from the community will be eagerly received!

A gentle introduction to the PSCIQUIC/RefNet packages is provided by a  Shiny app included inRefNet, which you can try out as demonstrated below.  Note, however, that this app is new and may not yet be as robust as an established  web app.  Clickable links to gene descriptions and PubMed abstracts are provided for all the interactions returned from your search.

 

library(shiny)
runApp(system.file("apps", package="RefNet"), port=9999)
Listening on http://127.0.0.1:9999 [1] initializing PSICQUIC...
[1] initializing RefNet from AnnotationHub...
[1] RefNet ready.
checking for biomart access...
  does ' http://www.biomart.org ' respond?
  creating ensembl mart
  hsapiens_gene_ensembl dataset provided?
connecting to biomart...

Bug reports, questions and suggestions are welcome.

 - Paul

ADD COMMENTlink modified 3.0 years ago • written 3.0 years ago by pshannon80
0
gravatar for Laurent Gatto
3.0 years ago by
Laurent Gatto840
United Kingdom
Laurent Gatto840 wrote:

Dear Paul,

Here is what I get:

> suppressPackageStartupMessages(library("RefNet"))
> runApp(system.file(package="RefNet", "apps"), port=9999)

Listening on http://127.0.0.1:9999
[1] initializing PSICQUIC...
[1] initializing RefNet from AnnotationHub...
Error in filters(ah) <- list(DataProvider = "RefNet") : 
  could not find function "filters<-"
^C
> traceback()
4: Sys.sleep(0.001)
3: withCallingHandlers(expr, error = function(e) {
       handle <- getOption("shiny.error")
       if (is.function(handle)) 
           handle()
   })
2: shinyCallingHandlers(while (!.globals$stopped) {
       serviceApp()
       Sys.sleep(0.001)
   })
1: runApp(system.file(package = "RefNet", "apps"), port = 9999)
> sessionInfo()
R Under development (unstable) (2014-11-01 r66923)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8    
 [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8   
 [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] RefNet_1.3.0         shiny_0.10.2.1       RCurl_1.95-4.3      
 [4] bitops_1.0-6         AnnotationHub_1.99.1 PSICQUIC_1.5.2      
 [7] plyr_1.8.1           httr_0.5             biomaRt_2.23.0      
[10] IRanges_2.1.4        S4Vectors_0.5.2      BiocGenerics_0.13.0 

loaded via a namespace (and not attached):
 [1] AnnotationDbi_1.29.1         Biobase_2.27.0              
 [3] BiocInstaller_1.17.1         DBI_0.3.1                   
 [5] digest_0.6.4                 GenomeInfoDb_1.3.6          
 [7] htmltools_0.2.6              httpuv_1.3.2                
 [9] interactiveDisplayBase_1.5.1 mime_0.2                    
[11] R6_2.0.1                     Rcpp_0.11.3                 
[13] RJSONIO_1.3-0                RSQLite_1.0.0               
[15] stringr_0.6.2                tools_3.2.0                 
[17] XML_3.98-1.1                 xtable_1.7-4                
ADD COMMENTlink written 3.0 years ago by Laurent Gatto840

RefNet needs to be updated in devel after some heavy changes to the API of AnnotationnHub. We'll do this very soon. In the meantime, I've verified that the shiny app in RefNet works in release. 

ADD REPLYlink written 3.0 years ago by Dan Tenenbaum ♦♦ 8.2k

Thanks for the clarification.

ADD REPLYlink written 3.0 years ago by Laurent Gatto840

Thanks pshannon, you give effective coding which is helpful for me to work as a developer in a web application development company.

ADD REPLYlink written 2.4 years ago by jamesmartin0570
0
gravatar for Grimes Mark
3.0 years ago by
Grimes Mark40
United States
Grimes Mark40 wrote:

Paul

 

Copied and pasted from your post:

runApp(system.file(package="RefNet", "apps"), port=9999))

Error: unexpected ')' in "runApp(system.file(package="RefNet", "apps"), port=9999))"

Odd error. Try this

runApp(system.file(package="RefNet", "apps"), port=9999)

Error: could not find function "runApp"

shiny::runApp(system.file(package="RefNet", "apps"), port=9999)

Loading required package: shiny

Error in shinyAppDir(x) : No Shiny application exists at the path ""

> sessionInfo()
R version 3.1.1 (2014-07-10)
Platform: x86_64-apple-darwin13.1.0 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
 [1] parallel  splines   grid      stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] shiny_0.10.2.1       rgl_0.93.1098        plyr_1.8.1           RefNet_1.0.4         RCurl_1.95-4.3       bitops_1.0-6         AnnotationHub_1.4.0 
 [8] PSICQUIC_1.2.1       biomaRt_2.20.0       Biostrings_2.32.1    XVector_0.4.0        IRanges_1.22.10      GOstats_2.30.0       Category_2.30.0     
[15] Matrix_1.1-4         GO.db_2.14.0         org.Hs.eg.db_2.14.0  RSQLite_1.0.0        DBI_0.3.1            AnnotationDbi_1.26.1 GenomeInfoDb_1.0.2  
[22] Biobase_2.24.0       BiocGenerics_0.10.0  RCytoscape_1.14.0    XMLRPC_0.3-0         graph_1.42.0         devtools_1.6.1       gplots_2.14.2       
[29] Rtsne_0.9            tsne_0.1-2           vegan_2.0-10         permute_0.8-3        RUnit_0.4.27         adegenet_1.4-2       ade4_1.6-2          
[36] cluster_1.15.3       Hmisc_3.14-5         Formula_1.1-2        survival_2.37-7      lattice_0.20-29      stringr_0.6.2        fdrtool_1.2.12      
[43] qgraph_1.2.5        

loaded via a namespace (and not attached):
 [1] acepack_1.3-3.3          annotate_1.42.1          AnnotationForge_1.6.1    ape_3.1-4                BiocInstaller_1.16.0     caTools_1.17.1          
 [7] colorspace_1.2-4         corpcor_1.6.7            digest_0.6.4             ellipse_0.3-8            foreign_0.8-61           gdata_2.13.3            
[13] genefilter_1.46.1        GenomicRanges_1.16.4     ggplot2_1.0.0            glasso_1.8               gridSVG_1.4-0            GSEABase_1.26.0         
[19] gtable_0.1.2             gtools_3.4.1             htmltools_0.2.6          httpuv_1.3.2             httr_0.5                 huge_1.2.6              
[25] igraph_0.7.1             interactiveDisplay_1.2.0 jpeg_0.1-8               KernSmooth_2.23-13       latticeExtra_0.6-26      lavaan_0.5-17           
[31] MASS_7.3-35              matrixcalc_1.0-3         mime_0.2                 mnormt_1.5-1             munsell_0.4.2            nlme_3.1-118            
[37] nnet_7.3-8               pbivnorm_0.5-1           png_0.1-7                proto_0.3-10             psych_1.4.8.11           quadprog_1.5-5          
[43] R6_2.0.1                 RBGL_1.40.1              RColorBrewer_1.0-5       Rcpp_0.11.3              reshape2_1.4             rjson_0.2.14            
[49] RJSONIO_1.3-0            rpart_4.1-8              scales_0.2.4             sem_3.1-5                sna_2.3-2                stats4_3.1.1            
[55] tools_3.1.1              XML_3.98-1.1             xtable_1.7-4             zlibbioc_1.10.0         
> ?shiny
> suppressPackageStartupMessages(library("RefNet"))
> runApp(system.file(package="RefNet", "apps"), port=9999)
Error in shinyAppDir(x) : No Shiny application exists at the path ""
> traceback()
5: stop("No Shiny application exists at the path \"", appDir, "\"")
4: shinyAppDir(x)
3: as.shiny.appobj.character(appDir)
2: as.shiny.appobj(appDir)
1: runApp(system.file(package = "RefNet", "apps"), port = 9999)

Mark

 

ADD COMMENTlink written 3.0 years ago by Grimes Mark40

I've modified the answer to provide the correct code.

ADD REPLYlink written 3.0 years ago by Dan Tenenbaum ♦♦ 8.2k
0
gravatar for pshannon
3.0 years ago by
pshannon80
United States
pshannon80 wrote:

Hi Mark,

Thanks for keeping at this.  

You have an out-of-date copy of RefNet.  You need version 1.2.0.  Please try this in your R session:

source("http://bioconductor.org/biocLite.R")
biocLite("RefNet")
suppressPackageStartupMessages(library(RefNet))
dir(system.file(package="RefNet", "apps")

You should see:

"server.R" "ui.R"     "www" 

And finally this then should work:

runApp(system.file(package="RefNet", "apps"), port=9999)

 

ADD COMMENTlink written 3.0 years ago by pshannon80
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