R/create_variables_all.R

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

#'\code{create_variables_all}
#'
#'This function returns the identifiers of all the variables used in the ILP 
#'formulation together with an explanation about the meaning of each of them. 
#'Also it returns a list of useful identifiers.
#'
#'Enio Gjerga, 2020

create_variables_all <- function(pknList=pknList, dataMatrix=dataMatrix){

  ## ======================================= ##
  ## ======= Load create_variables.R ======= ##
  ## ======================================= ##

  create_variables <- function(pknList=pknList, dataMatrix = dataMatrix, 
                               conditionIDX=conditionIDX){

    colnames(pknList) <- c("X1", "X2", "X3")

    nodes <- paste0("xb", 1:(nrow(dataMatrix$dataMatrix)*
                               ncol(dataMatrix$dataMatrix)), 
                    "_", conditionIDX)
    nodesUp <- paste0("xb", (nrow(dataMatrix$dataMatrix)*
                               ncol(dataMatrix$dataMatrix)+1):
                        (2*nrow(dataMatrix$dataMatrix)*
                           ncol(dataMatrix$dataMatrix)), 
                      "_", conditionIDX)
    nodesDown <- paste0("xb", (2*nrow(dataMatrix$dataMatrix)*
                                 ncol(dataMatrix$dataMatrix)+1):
                          (3*nrow(dataMatrix$dataMatrix)*
                             ncol(dataMatrix$dataMatrix)), 
                        "_", conditionIDX)

    expNodes <- c()
    expNodesUp <- c()
    expNodesDown <- c()
    expNodesReduced <- c()
    expNodesReducedUpSource <- c()
    expNodesReducedDownSource <- c()
    expNodesReducedUpTarget <- c()
    expNodesReducedDownTarget <- c()
    idxExperimentNodes <- c()
    for(i in 1:nrow(dataMatrix$dataMatrix)){

      expNodes <- c(expNodes, paste0("Species ", dataMatrix$species, 
                                     " in experiment ", conditionIDX))
      expNodesReduced = c(expNodesReduced, paste0("Species ", 
                                                  dataMatrix$species))
      expNodesUp <- c(expNodesUp, paste0("SpeciesUP ", dataMatrix$species, 
                                         " in experiment ", conditionIDX))
      expNodesDown <- c(expNodesDown, paste0("SpeciesDown ", dataMatrix$species, 
                                             " in experiment ", conditionIDX))
      expNodesReducedUpSource <- c(expNodesReducedUpSource, 
                                   as.character(pknList$X1))
      expNodesReducedDownSource <- c(expNodesReducedDownSource, 
                                     as.character(pknList$X1))
      expNodesReducedUpTarget <- c(expNodesReducedUpTarget, 
                                   as.character(pknList$X3))
      expNodesReducedDownTarget <- c(expNodesReducedDownTarget, 
                                     as.character(pknList$X3))

      idxExperimentNodes <- c(idxExperimentNodes, length(expNodes))

    }

    nodesALL <- c(nodes, nodesUp, nodesDown)
    expNodesALL <- c(expNodes, expNodesUp, expNodesDown)

    idxNodes <- 1:(nrow(dataMatrix$dataMatrix)*ncol(dataMatrix$dataMatrix))
    idxNodesUp <- (nrow(dataMatrix$dataMatrix)*ncol(dataMatrix$dataMatrix)+1):
      (2*nrow(dataMatrix$dataMatrix)*ncol(dataMatrix$dataMatrix))
    idxNodesDown <- (2*nrow(dataMatrix$dataMatrix)*ncol(dataMatrix$dataMatrix)+1):
      (3*nrow(dataMatrix$dataMatrix)*ncol(dataMatrix$dataMatrix))

    # edges
    edgesUp <- paste0("xb", (length(nodesALL)+1):(length(nodesALL)+
                                                    nrow(pknList)*
                                                    nrow(dataMatrix$dataMatrix)), 
                      "_", conditionIDX)
    edgesDown <- paste0("xb", (length(nodesALL)+
                                 nrow(pknList)*nrow(dataMatrix$dataMatrix)+1):
                          (length(nodesALL)+nrow(pknList)*
                             nrow(dataMatrix$dataMatrix)+nrow(pknList)*
                             nrow(dataMatrix$dataMatrix)), "_", conditionIDX)

    expEdgesUp <- c()
    expEdgesDown <- c()
    expEdgesReducedSource <- c()
    expEdgesReducedTarget <- c()
    idxExperimentEdges <- c()
    expNodesReducedUp <- c()
    expNodesReducedDown <- c()
    for(i in 1:nrow(dataMatrix$dataMatrix)){

      expEdgesUp <- c(expEdgesUp, paste0("ReactionUp ", 
                                         as.character(pknList$X1), "=", 
                                         as.character(pknList$X3), 
                                         " in experiment ", conditionIDX))
      expEdgesDown <- c(expEdgesDown, paste0("ReactionDown ", 
                                             as.character(pknList$X1), "=", 
                                             as.character(pknList$X3), 
                                             " in experiment ", conditionIDX))
      expEdgesReducedSource <- c(expEdgesReducedSource, 
                                 paste0("ReactionSource ", 
                                        as.character(pknList$X1)))
      expEdgesReducedTarget <- c(expEdgesReducedTarget, 
                                 paste0("ReactionTarget ", 
                                        as.character(pknList$X3)))
      expNodesReducedUp <- c(expNodesReducedUp, pknList$X1)
      expNodesReducedDown <- c(expNodesReducedDown, pknList$X3)

      idxExperimentEdges <- c(idxExperimentEdges, length(expEdgesUp))

    }

    edgesALL <- c(edgesUp, edgesDown)
    expEdgesALL <- c(expEdgesUp, expEdgesDown)

    idxEdgesUp <- (length(nodesALL)+1):(length(nodesALL)+
                                          1+
                                          nrow(pknList)*
                                          nrow(dataMatrix$dataMatrix)-1)
    idxEdgesDown <- (length(nodesALL)+
                       1+nrow(pknList)*nrow(dataMatrix$dataMatrix)):
      (length(nodesALL)+1+nrow(pknList)*nrow(dataMatrix$dataMatrix)+
         nrow(pknList)*nrow(dataMatrix$dataMatrix)-1)

    signs <- pknList$X2
    reactionSource <- as.character(pknList$X1)
    reactionTarget <- as.character(pknList$X3)
    if(nrow(dataMatrix$dataMatrix) > 1){

      for(i in 2:nrow(dataMatrix$dataMatrix)){

        signs <- c(signs, pknList$X2)
        reactionSource <- c(reactionSource, as.character(pknList$X1))
        reactionTarget <- c(reactionTarget, as.character(pknList$X3))

      }

    }

    ##
    #Introducing distance variables

    dist <- paste0("dist_", sapply(strsplit(expNodesALL[idxNodes], 
                                            split = " "), "[[", 2))

    distExp <- paste0("Distance ", sapply(strsplit(expNodesALL[idxNodes],
                                                   split = " "), "[[", 2))

    ##
    #Introducing B variables

    varB <- paste0("B_", sapply(strsplit(expNodes, split = " "),
                                function(x) x[2]), "_", conditionIDX)
    expVarB <- paste0("B variable for ", sapply(strsplit(expNodes, split = " "),
                                                function(x) x[2]), 
                      " in experiment ", conditionIDX)

    ##
    #Matching table for u variables
    uTable <- matrix(data = , nrow = length(idxEdgesUp), ncol = 2)
    uTable[, 1] <- c(nodesALL, edgesALL, varB, dist)[idxEdgesUp]
    uTable[, 2] <- c(nodesALL, edgesALL, varB, dist)[idxEdgesDown]


    # output
    res <- list(variables=c(nodesALL, edgesALL, varB, dist), 
                exp=c(expNodesALL, expEdgesALL, expVarB, distExp), 
                idxNodes=idxNodes, idxNodesUp=idxNodesUp,
                idxNodesDown=idxNodesDown, idxEdgesUp=idxEdgesUp, 
                idxEdgesDown=idxEdgesDown, signs=signs,
                reactionSource=reactionSource, reactionTarget=reactionTarget, 
                expNodesReduced=expNodesReduced,
                expNodesReducedUpSource=expNodesReducedUpSource, 
                expNodesReducedDownSource=expNodesReducedDownSource,
                expNodesReducedDownTarget=expNodesReducedDownTarget, 
                expNodesReducedUpTarget=expNodesReducedUpTarget,
                expEdgesReducedSource=expEdgesReducedSource, 
                expEdgesReducedTarget=expEdgesReducedTarget,
                idxExperimentNodes=idxExperimentNodes, 
                idxExperimentEdges=idxExperimentEdges,
                expNodesReducedUp=expNodesReducedUp, 
                expNodesReducedDown=expNodesReducedDown, 
                idxB = (length(c(nodesALL, edgesALL))+1):
                  (length(c(nodesALL, edgesALL))+length(varB)),
                idxDist = (length(c(nodesALL, edgesALL))+length(varB)+1):
                  (length(c(nodesALL, edgesALL))+length(varB)+length(dist)), 
                uTable = uTable)

    return(res)

  }

  res <- list()
  namesRes <- c()

  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, ]))

    res[[length(res)+1]] <- create_variables(pknList = pknList, dataMatrix = dM, 
                                             conditionIDX = i)

    namesRes <- c(namesRes, paste0("Condition_", i))

  }

  names(res) <- namesRes

  return(res)

}