R/write_objective_function_all.R

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

#'\code{write_objective_function_all}
#'
#'This code writes the objective function of the ILP problem for all the 
#'conditions.
#'
#'Enio Gjerga, 2020

write_objective_function_all <- function(dataMatrix = dataMatrix, 
                                         variables = variables, 
                                         alphaWeight=alphaWeight, 
                                         betaWeight=betaWeight,scores=scores, 
                                         measWeights=measWeights, 
                                         conditionIDX = conditionIDX ) {
  
  ## ======================================= ##
  ## === Load write_objective_function.R === ##
  ## ======================================= ##
  
  write_objective_function <- function(dataMatrix = dataMatrix, 
                                       variables = variables, 
                                       alphaWeight=alphaWeight, 
                                       betaWeight=betaWeight, 
                                       scores = scores, 
                                       measWeights = measWeights, 
                                       conditionIDX = conditionIDX ){
    
    if(is.null(scores)){
      
      measured <- gsub(colnames(dataMatrix$dataMatrix)[dataMatrix$dsID], 
                       pattern = "DS:", replacement = "")
      
      idxMeasured <- c()
      for(i in 1:length(measured)){
        
        idxMeasured <- c(idxMeasured, which(variables$expNodesReduced==
                                              paste0("Species ", measured[i])))
        
      }
      
      measuredVar <- variables$variables[idxMeasured]
      
      allWeights <- rep(x = 0, length(measuredVar))
      
      if(!is.null(measWeights)){
        
        weightedSpecies <- colnames(measWeights)
        
        for(i in 1:length(weightedSpecies)){
          
          allWeights[which(which(variables$expNodesReduced==
                                   paste0("Species ", weightedSpecies[i]))==
                             idxMeasured)] <- measWeights[i]
          
        }
        
        objectiveFunctionVec <- paste0(" + ", allWeights, " absDiff", 
                                       gsub(measuredVar, pattern = "xb", 
                                            replacement = ""))
        
      } else {
        
        objectiveFunctionVec <- paste0(" + ", alphaWeight, " absDiff", 
                                       gsub(measuredVar, pattern = "xb", 
                                            replacement = ""))
        
      }
      
      objectiveFunction <- paste(objectiveFunctionVec, collapse = "")
      
      objectiveFunction <- substring(text = objectiveFunction[1], first = 4, 
                                     last = nchar(objectiveFunction))
      
      objectiveFunction <- paste0("", objectiveFunction)
      
      objectiveFunctionUpVec <- paste0(
        " + ", betaWeight, " ", variables$variables[variables$idxNodesUp])
      objectiveFunctionUp <- paste(objectiveFunctionUpVec, collapse = "")
      
      objectiveFunctionDownVec <- paste0(
        " + ", betaWeight, " ", variables$variables[variables$idxNodesDown])
      objectiveFunctionDown <- paste(objectiveFunctionDownVec, collapse = "")
      
      objectiveFunction <- paste0(objectiveFunction, objectiveFunctionUp)
      objectiveFunction <- paste0(objectiveFunction, objectiveFunctionDown)
      
      return(objectiveFunction)
      
    } else {
      
      measured <- gsub(colnames(dataMatrix$dataMatrix)[dataMatrix$dsID], 
                       pattern = "DS:", replacement = "")
      
      idxMeasured <- c()
      for(i in 1:length(measured)){
        
        idxMeasured <- c(idxMeasured, which(variables$expNodesReduced==
                                              paste0("Species ", measured[i])))
        
      }
      
      measuredVar <- variables$variables[idxMeasured]
      
      allWeights <- rep(x = 0, length(measuredVar))
      
      if(!is.null(measWeights)){
        
        weightedSpecies <- colnames(measWeights)
        
        for(i in 1:length(weightedSpecies)){
          
          allWeights[which(which(variables$expNodesReduced==
                                   paste0("Species ", weightedSpecies[i]))==
                             idxMeasured)] <- measWeights[i]
          
        }
        
        objectiveFunctionVec <- paste0(" + ", allWeights, " absDiff", 
                                       gsub(measuredVar, pattern = "xb", 
                                            replacement = ""))
        
      } else {
        
        objectiveFunctionVec <- paste0(" + ", alphaWeight, " absDiff", 
                                       gsub(measuredVar, pattern = "xb", 
                                            replacement = ""))
        
      }
      objectiveFunction <- paste(objectiveFunctionVec, collapse = "")
      
      objectiveFunction <- substring(text = objectiveFunction[1], first = 4, 
                                     last = nchar(objectiveFunction))
      
      objectiveFunction <- paste0("", objectiveFunction)
      
      betaValPos <- rep(betaWeight, length(variables$idxNodesUp))
      betaValNeg <- rep(betaWeight, length(variables$idxNodesDown))
      
      #
      idxPos <- which(scores[1, ] >= 0)
      if(length(idxPos) > 0){
        
        speciesPos <- colnames(scores)[idxPos]
        
        for(ii in 1:length(speciesPos)){
          
          currPos <- speciesPos[ii]
          
          idx <- which(variables$exp[variables$idxNodesUp]==
                         paste0("SpeciesUP ", currPos, " in experiment ", 
                                conditionIDX))
          betaValPos[idx] <- betaWeight*(1-scores[1, idxPos[ii]])
          
          idx <- which(variables$exp[variables$idxNodesDown]==
                         paste0("SpeciesDown ", currPos, " in experiment ", 
                                conditionIDX))
          betaValNeg[idx] <- betaWeight*(1+scores[1, idxPos[ii]])
          
        }
        
      }
      
      #
      idxNeg <- which(scores[1, ] < 0)
      if(length(idxNeg) > 0){
        
        speciesNeg <- colnames(scores)[idxNeg]
        
        for(ii in 1:length(speciesNeg)){
          
          currNeg <- speciesNeg[ii]
          
          idx <- which(variables$exp[variables$idxNodesUp]==
                         paste0("SpeciesUP ", currNeg, " in experiment ", 
                                conditionIDX))
          betaValPos[idx] <- betaWeight*(1-scores[1, idxNeg[ii]])
          
          idx <- which(variables$exp[variables$idxNodesDown]==
                         paste0("SpeciesDown ", currNeg, " in experiment ", 
                                conditionIDX))
          betaValNeg[idx] <- betaWeight*(1+scores[1, idxNeg[ii]])
          
        }
        
      }
      
      objectiveFunctionUpVec <- paste0(
        " + ", betaValPos, " ", variables$variables[variables$idxNodesUp])
      objectiveFunctionUp <- paste(objectiveFunctionUpVec, collapse = "")
      
      objectiveFunctionDownVec <- paste0(
        " + ", betaValNeg, " ", variables$variables[variables$idxNodesDown])
      objectiveFunctionDown <- paste(objectiveFunctionDownVec, collapse = "")
      
      objectiveFunction <- paste0(objectiveFunction, objectiveFunctionUp)
      objectiveFunction <- paste0(objectiveFunction, objectiveFunctionDown)
      
      return(objectiveFunction)
      
    }
    
  }
  
  OF <- "Obj:\t "
  
  if(!is.null(measWeights)){
    
    if(nrow(measWeights)!=nrow(dataMatrix$dataMatrix)){
      
      stop("Number of rows of the Measurements-Weights table should be the same 
           as the number of conditions considered..")
      
    }
    
  }
  
  for (i in 1:nrow(dataMatrix$dataMatrix)) {
    
    dM <- dataMatrix
    dM$dataMatrix <- as.matrix(t(dataMatrix$dataMatrix[i, ]))
    dM$dataMatrixSign <- as.matrix(t(dataMatrix$dataMatrixSign[i, ]))
    
    if(!is.null(measWeights)){
      
      mm <- as.matrix(measWeights[i, ])
      
    } else {
      
      mm <- NULL
      
    }
    # print(mm)
    
    var <- variables[[i]]
    if (i==1) {
      OF <- paste0(OF, write_objective_function(dataMatrix = dM, 
                                                variables = var, 
                                                alphaWeight=alphaWeight, 
                                                betaWeight = betaWeight,
                                                scores=scores,measWeights = mm,
                                                conditionIDX=i))
    } else {
      OF <- paste0(OF, " + ",  write_objective_function(dataMatrix = dM, 
                                                        variables = var, 
                                                        alphaWeight=alphaWeight, 
                                                        betaWeight = betaWeight,
                                                        scores=scores,
                                                        measWeights = mm,
                                                        conditionIDX=i))
    }
    
  }
  
  return(OF)
  
}