inst/scripts/STRINGExplore_PHALY-Example.R

In hyginn/BCB420.2019.ESA: Exploratory Systems Analysis Tools

#### Versions ####
# v 2.0 : functionalized example of tool output and usage
# v 1.0 : complete code for creating interactive viz, in script form
# v 0.1 : static coexpression igraph, using coexpression data;
#         separate list of protein actions related to edges
####
# Worked example of STRINGExplore with PHALY system

#### Setup and Dependencies ####
# Package requirements
require(igraph, quietly = TRUE)
require(magrittr, quietly = TRUE)
require(igraph, quietly = TRUE)
require(visNetwork, quietly=TRUE)
require(R.filesets, quietly=TRUE)

# Internal functions
source("./R/STRINGExplore.R")
source("./R/fetchData.R")
source("./R/fetchComponents.R")


# fetchComponents is used in place of simply the system name to
# allow flexibility of input to the user-- for example, the possiblity
# of exploring a subsystem or simply a list of known HGNC symbols of interest,
# rather than one of the prepared curations
# PHALYnetwork
PHALYnetwork <- STRINGExplore("PHALY")
head(PHALYnetwork$nodes) # The dataframe of node information. Call to view the network nodes
head(PHALYnetwork$edges) # The dataframe of edge information. Call to view the network edges and protein interaction info
PHALYnetwork$network # The visNetwork object. Call to plot the network in your RStudio

# [END]