# clusterSystemsScript.R
#
# Purpose: Script that generates the example results
# used in my project page.
# Version: 1.0
# Date: April 1 2019
# Author: Rachel Silverstein
# License: MIT
#
# ==============================================================================
# NO SIDE EFFECTS:
# This script can be safely source()'d to define the functions it contains and
# install.packages()/run library() as required.
# All other code will not be executed unless this is done interactively.
# ==== PACKAGES ==============================================================
if (require("cluster")) {
install.packages(cluster)
}
library(cluster)
if (require("igraph")) {
install.packages(igraph)
}
library(igraph)
if (require("VennDiagram")) {
install.packages(VennDiagram)
}
library(VennDiagram)
# ==== FUNCTIONS =============================================================
source("./R/clusterSystems.R")
# ==== PROCESS ===============================================================
if (FALSE) {
myDB <- fetchData("SysDB")
rootSysIDs <- SyDBgetRootSysIDs(myDB)
sys_names <- names(rootSysIDs)
# initialize a list of the genes in the different systems
systems <- vector(mode="list", length=length(sys_names))
names(systems) <- sys_names
# populate the list with vectors of genes
for (i in seq_along(sys_names)) {
systems[[i]] <- SyDBgetSysSymbols(myDB, sys_names[i])
}
# test clustering by variables individually
clusterSystems(systems,
distances = c("transcription_factor"))
clusterSystems(systems,
distances = c("expression_profile"))
clusterSystems(systems,
distances = c("network_jaccard"))
clusterSystems(systems,
distances = c("network_distance"))
# test some combinations
clusterSystems(systems,
distances = c("transcription_factor",
"network_jaccard",
"network_distance",
"expression_profile"),
combineMatrices = 'sum')
clusterSystems(systems,
distances = c("transcription_factor",
"network_jaccard",
"network_distance",
"expression_profile"),
combineMatrices = 'product')
clusterSystems(systems,
distances = c("transcription_factor",
"network_jaccard",
"network_distance",
"expression_profile"),
combineMatrices = 'minimum')
clusterSystems(systems,
distances = c("transcription_factor",
"network_jaccard",
"network_distance",
"expression_profile"),
combineMatrices = 'maximum')
}
# [END]
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