R/write_constraints_8.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 (8) of the ILP problem for all the 
## conditions.
## 
## Enio Gjerga, 2020

write_constraints_8 <- function(variables=variables, 
                                inputs=inputs, 
                                pknList=pknList){
  
  ## constraints8 <- c()
  ## 
  ## for(ii in seq_len(length(variables))){
  ##   
  ##   ##
  ##   cc <- paste0(
  ##     variables[[ii]]$variables[variables[[ii]]$idxNodesUp], 
  ##     " - ", 
  ##     variables[[ii]]$variables[variables[[ii]]$idxNodesDown], 
  ##                " + ", variables[[ii]]$variables[variables[[ii]]$idxB], 
  ##     " - ", variables[[ii]]$variables[variables[[ii]]$idxNodes], " = 0")
  ##   
  ##   constraints8 <- c(constraints8, cc)
  ##   
  ##   ##
  ##   kk <- paste0("Species ", colnames(inputs), " in experiment ", ii)
  ##   cc <- paste0(
  ##     variables[[ii]]$variables[variables[[ii]]$idxB[which(
  ##       !(variables[[ii]]$exp[variables[[ii]]$idxNodes] %in% kk))]], " = 0")
  ##   constraints8 <- c(constraints8, cc)
  ##   
  ##   ##
  ##   kk <- paste0("Species ", colnames(inputs), " in experiment ", ii)
  ##   cc= c()
  ##   for(jj in seq_len(length(kk))){
  ##     cName = strsplit(x = kk[jj], split = " ")[[1]][2]
  ##     cc = c(cc, paste0(
  ##       variables[[ii]]$variables[which(
  ##         variables[[ii]]$exp==paste0(
  ##           "Species ", cName, " in experiment ", ii))], " = ", inputs[ii, jj]))
  ##   }
  ##   constraints8 <- c(constraints8, cc)
  ##   
  ##   ##
  ##   if (length(
  ##     setdiff(
  ##       as.character(pknList[, 1]), 
  ##       as.character(pknList[, 3])))>0) {
  ##     kk <- paste0(
  ##       "Species ", 
  ##       setdiff(as.character(pknList[, 1]), 
  ##               as.character(pknList[, 3])), " in experiment ", ii)
  ##     cc <- paste0(
  ##       variables[[ii]]$variables[variables[[ii]]$idxNodes[which(
  ##         variables[[ii]]$exp[variables[[ii]]$idxNodes] %in% kk)]], " - ", 
  ##                  variables[[ii]]$variables[variables[[ii]]$idxB[which(
  ##                   variables[[ii]]$exp[variables[[ii]]$idxNodes] %in% kk)]], 
  ##       " = 0")
  ##     constraints8 <- c(constraints8, cc)
  ##   }
  ##   
  ## }
  
  ii=1
  ##
  cc1 <- paste0(
    variables[[ii]]$variables[variables[[ii]]$idxNodesUp], 
    " - ", 
    variables[[ii]]$variables[variables[[ii]]$idxNodesDown], 
    " + ", variables[[ii]]$variables[variables[[ii]]$idxB], 
    " - ", variables[[ii]]$variables[variables[[ii]]$idxNodes], " = 0")
  
  ## constraints8 <- c(constraints8, cc)
  
  ##
  kk <- paste0("Species ", colnames(inputs), " in experiment ", ii)
  cc2 <- paste0(
    variables[[ii]]$variables[variables[[ii]]$idxB[which(
      !(variables[[ii]]$exp[variables[[ii]]$idxNodes] %in% kk))]], " = 0")
  ## constraints8 <- c(constraints8, cc)
  
  ##
  kk <- paste0("Species ", colnames(inputs), " in experiment ", ii)
  cc3= c()
  for(jj in seq_len(length(kk))){
    cName = strsplit(x = kk[jj], split = " ")[[1]][2]
    cc3 = c(cc3, paste0(
      variables[[ii]]$variables[which(
        variables[[ii]]$exp==paste0(
          "Species ", cName, " in experiment ", ii))], " = ", inputs[ii, jj]))
  }
  ## constraints8 <- c(constraints8, cc)
  
  ##
  if (length(
    setdiff(
      as.character(pknList[, 1]), 
      as.character(pknList[, 3])))>0) {
    kk <- paste0(
      "Species ", 
      setdiff(as.character(pknList[, 1]), 
              as.character(pknList[, 3])), " in experiment ", ii)
    cc4 <- paste0(
      variables[[ii]]$variables[variables[[ii]]$idxNodes[which(
        variables[[ii]]$exp[variables[[ii]]$idxNodes] %in% kk)]], " - ", 
      variables[[ii]]$variables[variables[[ii]]$idxB[which(
        variables[[ii]]$exp[variables[[ii]]$idxNodes] %in% kk)]], 
      " = 0")
    ## constraints8 <- c(constraints8, cc)
  }
  
  constraints8 <- c(cc1, cc2, cc3, cc4)
  
  return(constraints8)
  
}