R/write_constraints_7.R

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

## This code writes the list of constraints (7) of the ILP problem for all the
## conditions.
##
##
## Enio Gjerga, 2020

write_constraints_7 <- function(variables=variables,
                                dataMatrix=dataMatrix,
                                inputs = inputs,
                                pknList = pknList) {

  ##library(igraph)
  ##requireNamespace("igraph")
  constraints7 <- c()

  for(ii in seq_len(length(variables))){

    source <- unique(variables[[ii]]$reactionSource)
    target <- unique(variables[[ii]]$reactionTarget)

    gg <- igraph::graph_from_data_frame(d = pknList[, c(3, 1)])
    adj <- igraph::get.adjacency(gg)
    adj <- as.matrix(adj)

    idx1 <- which(rowSums(adj)==0)
    idx2 <- setdiff(seq_len(nrow(adj)), idx1)

    if (length(idx1)>0) {
      constraints7 <-
        c(constraints7,
          paste0(
            variables[[ii]]$variables[which(
              variables[[ii]]$exp%in%paste0(
                "SpeciesDown ",
                rownames(adj)[idx1], " in experiment ", ii))], " <= 0"))
    }

    for(i in seq_len(length(idx2))){

      cc <- paste0(
        variables[[ii]]$variables[which(
          variables[[ii]]$exp==paste0(
            "SpeciesDown ",
            rownames(adj)[idx2[i]], " in experiment ", ii))],
                   paste(
                     paste0(
                       " - ",
                       variables[[ii]]$variables[which(
                         variables[[ii]]$exp%in%paste0(
                           "ReactionDown ",
                           colnames(adj)[which(adj[idx2[i], ]>0)],
                           "=", rownames(adj)[idx2[i]],
                           " in experiment ", ii))]), collapse = ""), " <= 0")

      constraints7 <- c(constraints7, cc)

    }

  }
  
  ##
  ii=1
  source <- unique(variables[[ii]]$reactionSource)
  target <- unique(variables[[ii]]$reactionTarget)
  
  gg <- igraph::graph_from_data_frame(d = pknList[, c(3, 1)])
  adj <- igraph::get.adjacency(gg)
  adj <- as.matrix(adj)
  
  idx1 <- which(rowSums(adj)==0)
  idx2 <- setdiff(seq_len(nrow(adj)), idx1)
  
  if (length(idx1)>0) {
    cc1 <-
      paste0(
          variables[[ii]]$variables[which(
            variables[[ii]]$exp%in%paste0(
              "SpeciesDown ",
              rownames(adj)[idx1], " in experiment ", ii))], " <= 0")
  }
  
  cc2 <- rep("", length(idx2))
  for(i in seq_len(length(idx2))){
    
    cc2[i] <- paste0(
      variables[[ii]]$variables[which(
        variables[[ii]]$exp==paste0(
          "SpeciesDown ",
          rownames(adj)[idx2[i]], " in experiment ", ii))],
      paste(
        paste0(
          " - ",
          variables[[ii]]$variables[which(
            variables[[ii]]$exp%in%paste0(
              "ReactionDown ",
              colnames(adj)[which(adj[idx2[i], ]>0)],
              "=", rownames(adj)[idx2[i]],
              " in experiment ", ii))]), collapse = ""), " <= 0")
    
    ## constraints7 <- c(constraints7, cc)
    
  }

  return(c(cc1, cc2))
}