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## ----include=FALSE------------------------------------------------------------ library(knitr) opts_chunk$set(tidy.opts=list(width.cutoff=70, args.newline = TRUE, arrow = TRUE), tidy=TRUE) ## ----include=FALSE, eval=FALSE------------------------------------------------ # ## for README update # rmarkdown::render( # "ndexr-vignette.Rmd", # rmarkdown::md_document( # variant = "markdown_github" # ), # output_file = "README_raw.md", # output_dir = "../../" # ) ## ----eval=FALSE--------------------------------------------------------------- # if (!requireNamespace("BiocManager", quietly=TRUE)){ # install.packages("BiocManager") # } # BiocManager::install("ndexr") # library(ndexr) ## ----eval=FALSE--------------------------------------------------------------- # require(devtools) # install_github("frankkramer-lab/ndexr") # library(ndexr) ## ----eval=FALSE--------------------------------------------------------------- # require(remotes) # install_github("frankkramer-lab/ndexr") # library(ndexr) ## ----include=FALSE------------------------------------------------------------ ## load the library! library(ndexr) ## login to the NDEx server ndexcon = ndex_connect() ## ----eval=FALSE--------------------------------------------------------------- # ## load the library! # library(ndexr) # # ## login to the NDEx server # ndexcon = ndex_connect("username", "password") # # ## search the networks for "EGFR" # networks <- ndex_find_networks(ndexcon, "EGFR") # head(networks, 3) ## ----echo=FALSE--------------------------------------------------------------- networks <- ndex_find_networks(ndexcon, "EGFR") head(networks, 3) ## ----------------------------------------------------------------------------- ## UUID of the first search result networkId <- networks[1,'externalId'] networkId ## get summary of the network ndex_network_get_summary(ndexcon, networkId) ## get the entire network as RCX object rcx <- ndex_get_network(ndexcon, networkId) ## show the content (aspects) of the network rcx$metaData ## ----eval=FALSE--------------------------------------------------------------- # ## upload network as a new network to the NDEx server # networkId <- ndex_create_network(ndexcon, rcx) # # ## do some other fancy stuff with the network, then # ## update the network on the server # networkId <- ndex_update_network(ndexcon, rcx) # # ## realize, you did bad things to the poor network, so better # ## delete it on the server # ndex_delete_network(ndexcon, networkId) ## ----eval=FALSE, tidy=FALSE--------------------------------------------------- # ## load the library # library(ndexr) # # ## connect anonymously # ndexcon <- ndex_connect() # # ## log in with user name and password # ndexconUser <- ndex_connect(username="username", password="password") # # ## specify the server # ndexconLocal <- ndex_connect( # username="username", # password="password", # host="localhost:8888/ndex/rest" # ) # # ## manually change the api and connection configuration # ndexcon13 <- ndex_connect(ndexConf=ndex_config$Version_1.3) ## ----results = "hide"--------------------------------------------------------- ## list networks on server networks <- ndex_find_networks(ndexcon) ## ----------------------------------------------------------------------------- names(networks) networks[1:5,c('name','externalId')] ## ----------------------------------------------------------------------------- ## list networks on server (same as previous) networks <- ndex_find_networks(ndexcon, start=0, size=5) ## search for "EGFR" networksEgfr <- ndex_find_networks(ndexcon, searchString="EGFR") ## same as previous networksEgfr <- ndex_find_networks(ndexcon, "EGFR") networksEgfr[1:3,] ## search for networks of a user networksOfUser <- ndex_find_networks(ndexcon, accountName="ndextutorials") networksOfUser[1:5,c('name','owner','externalId')] ## ----------------------------------------------------------------------------- ## UUID of the first search result networkId <- networksOfUser[1,'externalId'] ## get network summary networkSummary <- ndex_network_get_summary(ndexcon, networkId) names(networkSummary) networkSummary[c('name','externalId')] ## get the entire network as RCX object rcx <- ndex_get_network(ndexcon, networkId) rcx$metaData ## ----eval=FALSE--------------------------------------------------------------- # ## create a new network on server # networkId <- ndex_create_network(ndexcon, rcx) # # ## update a network on server # networkId <- ndex_update_network(ndexcon, rcx) # # ## same as previous # networkId <- ndex_update_network(ndexcon, rcx, networkId) ## ----eval=FALSE--------------------------------------------------------------- # ## deletes the network from the server # ndex_delete_network(ndexcon, networkId) ## ----eval=FALSE--------------------------------------------------------------- # ## load the library! # library(ndexr) # # ## login to the NDEx server # ndexcon = ndex_connect() # # ## retrieve pathways of user "nci-pid" # networks_pid <- ndex_find_networks(ndexcon, accountName="nci-pid") # # ## list retrieved network information (only the first 10 entries) # networks_pid[1:10,"name"] ## ----echo=FALSE--------------------------------------------------------------- networks_pid <- ndex_find_networks(ndexcon, accountName="nci-pid") networks_pid[1:10,"name"] ## ----------------------------------------------------------------------------- ## show information on the first pathways listed networks_pid[1,] ## ----eval=FALSE--------------------------------------------------------------- # ## retrieve network data # mynetwork = ndex_get_network(ndexcon, networks_pid[1,"externalId"]) # # ## visualize the network with RCX # RCX::visualize(mynetwork) ## ----------------------------------------------------------------------------- ## get meta-data for a network metadata = ndex_network_get_metadata(ndexcon, networkId) names(metadata) metadata[c('name','elementCount')] ## ----------------------------------------------------------------------------- ## get aspect "nodeCitations" for the network networkAttibutes = ndex_network_get_aspect(ndexcon, networkId, "networkAttributes") networkAttibutes ## ----eval=FALSE--------------------------------------------------------------- # ndex_network_update_profile(ndexcon, networkId, name="My network", version="1.3") # ndex_network_update_profile(ndexcon, networkId, description="Nothing to see here") ## ----eval=FALSE--------------------------------------------------------------- # ## show all user who have permission to a network # ndex_network_get_permission(ndexcon, networkId, 'user') # # ## show all groups who have permission to a network # ndex_network_get_permission(ndexcon, networkId, 'group') # # ## show all users with write access to a network # ndex_network_get_permission(ndexcon, networkId, 'user', 'WRITE') # # ## grant an user permission to a network # ndex_network_update_permission(ndexcon, networkId, user=someUserUuid, 'READ') # # ## change the permission of an user to the network # ndex_network_update_permission(ndexcon, networkId, user=someUserUuid, 'WRITE') # # ## withdraw the permission from an user # ndex_network_delete_permission(ndexcon, networkId, user=someUserUuid) ## ----eval=FALSE--------------------------------------------------------------- # ndex_network_set_systemProperties(ndexcon, networkId, visibility="PUBLIC") # ndex_network_set_systemProperties(ndexcon, networkId, visibility="PRIVATE") ## ----eval=FALSE--------------------------------------------------------------- # ndex_network_set_systemProperties(ndexcon, networkId, readOnly=TRUE) ## ----eval=FALSE--------------------------------------------------------------- # ndex_network_set_systemProperties(ndexcon, networkId, showcase=TRUE) # ndex_network_set_systemProperties(ndexcon, networkId, showcase=FALSE) # # change more than one property simultaneously # ndex_network_set_systemProperties(ndexcon, networkId, readOnly=TRUE, visibility="PUBLIC", showcase=TRUE) ## ----eval=FALSE--------------------------------------------------------------- # provenance = ndex_network_get_provenance(ndexcon, networkId) ## ----------------------------------------------------------------------------- names(ndex_config) str(ndex_config, max.level = 3) ## ----------------------------------------------------------------------------- names(ndex_config$Version_2.0) ## ----------------------------------------------------------------------------- # Copy an existing config custom_ndex_config = ndex_config$Version_2.0 # Change the host connection for a local NDEx server installation custom_ndex_config$connection$host ="localhost:8090" # Custom path to the REST api custom_ndex_config$connection$api ="/api/rest" # Change the REST path for the ndex_get_network function custom_ndex_config$api$network$get$url ="/custom/networks/#NETWORKID#" # Add some (default) parameters to the function custom_ndex_config$api$network$get$params$newParam = list(method="parameter", tag="someTag", default="someValue") ## ----eval=FALSE--------------------------------------------------------------- # yamlToRConfig = function(yamlFile='R/ndex_api_config.yml', rScriptFile='R/ndex_api_config.r', defaultHeader=ndex_conf_header){ # yamlObj = yaml::yaml.load_file(yamlFile) # rCodeTxt = paste0(defaultHeader, listToRCode(yamlObj)) # outFile = file(rScriptFile) # writeLines(rCodeTxt, outFile) # close(outFile) # } # # yamlToRConfig()