tests_local.R

In frankkramer-lab/ndexr: NDEx R client library

###load
require(devtools)
install_github("frankkramer-lab/ndexr@develop")
library(ndexr)

###connect anonymously
#ndexcon1 = ndex_connect(verbose=T)
###connect as test user
#ndexcon2 = ndex_connect(username="testacc", password="testacc", verbose=T)

ndexcon1 = ndex_connect(username="testacc", password="testacc", host='http://dev.ndexbio.org/v2', verbose=T)
ndexcon2 = ndex_connect(host='http://dev.ndexbio.org/v2', verbose=T)


###get network api
apidata1 = ndex_get_network.api(ndexcon1)
apidata2 = ndex_get_network.api(ndexcon2)

###find some networks containing p53
pws1 = ndexr::ndex_find_networks(ndexcon1,"p53")
pws2 = ndexr::ndex_find_networks(ndexcon2,"p53")
###dont find networks
is.null(ndexr::ndex_find_networks(ndexcon1,"sdjlbelglserglersg"))
is.null(ndexr::ndex_find_networks(ndexcon2,"sdjlbelglserglersg"))

###get complete network as RCX
rcx1 = ndex.get.complete.network(ndexcon1,pws1[1,"externalId"])
rcx2 = ndex.get.complete.network(ndexcon2,pws1[1,"externalId"])

###convert to ngraph
ngraph1 = ndex.RCX2ngraph(rcx1)

###plot ngraph - automatical layout, and coloring - do not expect beauty here.
plot(ngraph1, vertex.label=V(ngraph1)$n, edge.label=E(ngraph1)$i)

###convert ngraph to RCX
rcx_back1 = ndex.ngraph2RCX(ngraph1)


##test equality of conversion: # equals everywhere except for nodeAttributes "v". TODO: Fix this
for(i in names(rcx1)) {
  cat(i)
  cat(all.equal(rcx1[[i]], rcx_back1[[i]]))
  cat("\n")
}

###save RCX object to ndex server. "ndex.RCXasNewNetwork" cleans up ndexStatus, provenanceHistory, status aspects
uuid = ndex_create_network(ndexcon1, ndexr:::ndex.RCXasNewNetwork(rcx_back1))




####### TO FIX FOR API v2:
 ### lets run through all the p53 pathways NDEx - RCX - ngraph - RCX
# rcxlist=list()
# rcxconvlist=list()
# ngraphlist = list()
# for(i in pws1$externalId) {
#   rcxlist[[i]] = ndex.get.complete.network(ndexcon1,i)
#   ngraphlist[[i]] = ndex.RCX2ngraph(rcxlist[[i]])
#   rcxconvlist[[i]] = ndex.ngraph2RCX(ngraphlist[[i]])
# }
# ### plot the graphs - no beautification yet
# pdf(paper = "a4",file="../ndexr_testplot.pdf")
# for(i in names(ngraphlist)) {
#   g = ngraphlist[[i]]
#   plot(g, vertex.label=V(g)$n, edge.label=E(g)$i)
# }
# dev.off()