tests/testthat/test_createNodesVariables.R

In saezlab/CARNIVAL: A CAusal Reasoning tool for Network Identification (from gene expression data) using Integer VALue programming

### This script is a unit test for the function createNodesVariables
#
# Matteo Spatuzzi 2021

#Create Dummy Data
nodenames <- c(paste("Node", seq(1,5), sep = ""))
perturbations_1 <- c(1,-1, 1) 
names(perturbations_1) <- c(nodenames[1], nodenames[2], nodenames[3])

measurements_1 <- c(5)
names(measurements_1) <- c(nodenames[5])

priorKnowledgeNetwork_1 <- matrix( c(nodenames[1], 1, nodenames[4], 
                                     nodenames[2], 1, nodenames[4],
                                     nodenames[3], -1, nodenames[1],
                                     nodenames[3], -1, nodenames[2],
                                     nodenames[4], 1, nodenames[5]), 
                                     byrow = T, ncol = 3) %>% as.data.frame()
colnames(priorKnowledgeNetwork_1) = c("Node1", "sign", "Node2")

nodesVariables <- createNodesVariables( priorKnowledgeNetwork = priorKnowledgeNetwork_1,
                                        perturbations = perturbations_1, 
                                        measurements = measurements_1 )

nodesVariables_expected <- data.frame( nodes = c(paste("Node", seq(1, 5), sep = "")), 
                                       nodesVars = c(paste("n", seq(1, 5), sep = "")), 
                                       nodesUpVars = c(paste("nU", seq(1, 5), sep = "")),
                                       nodesDownVars = c(paste("nD", seq(1, 5), sep = "")),
                                       nodesActStateVars = c(paste("nAc", seq(1, 5), sep = "")),
                                       nodesDistanceVars = c(paste("nDs", seq(1, 5), sep = "")),
                                       nodesType = c("P", "P", "P", "", "M") )

test_that("Nodes variables check:", {
  expect_equal(nodesVariables_expected, nodesVariables)
})

nodesVariables = createNodesVariables( priorKnowledgeNetwork = priorKnowledgeNetwork_1,
                                       perturbations = perturbations_1, 
                                       measurements = measurements_1, 
                                       prefixes = c("nodes" = "N", "nodesUp" = "NU", 
                                                   "nodesDown" = "ND", 
                                                   "nodesActivationState" = "NAc",
                                                   "nodesDistance" = "NDs") )


nodesVariables_expected <- data.frame( nodes = c(paste("Node", seq(1,5), sep = "")), 
                                       nodesVars = c(paste("N", seq(1,5), sep = "")), 
                                       nodesUpVars = c(paste("NU", seq(1,5), sep = "")),
                                       nodesDownVars = c(paste("ND", seq(1,5), sep = "")),
                                       nodesActStateVars = c(paste("NAc", seq(1,5), sep = "")),
                                       nodesDistanceVars = c(paste("NDs", seq(1,5), sep = "")),
                                       nodesType = c("P", "P", "P", "", "M") )

test_that("Nodes variables check:", {
  expect_equal(nodesVariables_expected, nodesVariables)
})