R/write_experimental_conditions_constraints.R

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

#'\code{write_experimental_conditions_constraints}
#'
#' Writing the additional constraints when considering the multiple experimental 
#' conditions.
#'
#'Enio Gjerga, 2020
 
write_experimental_conditions_constraints <- function(variables = variables){
  
  constraint1 = c()
  for(jj in 1:length(variables$`Reaction Variables`$Explanation)){
    
    for(ii in 1:(length(variables)-1)){
      
      tt <- 
        strsplit(x = strsplit(
          x = variables[[ii]]$exp[variables[[ii]]$idxEdgesUp[jj]], split = " ", 
          fixed = TRUE)[[1]][2], split = "=", fixed = TRUE)[[1]][2]
      ss <- 
        strsplit(x = strsplit(
          x = variables[[ii]]$exp[variables[[ii]]$idxEdgesUp[jj]], split = " ", 
          fixed = TRUE)[[1]][2], split = "=", fixed = TRUE)[[1]][1]
      
      var_u_p <- variables[[ii]]$variables[variables[[ii]]$idxEdgesUp[jj]]
      var_x_p <- variables[[ii]]$variables[which(variables[[ii]]$exp==
                                                   paste0("SpeciesUP ", 
                                                          tt, 
                                                          " in experiment ", 
                                                          ii))]
      
      c1 = paste0("andP_", ss, "_", tt, "_", ii, " - ", 
                  var_u_p, " - ", var_x_p, " >= -1")
      c2 = paste0("andP_", ss, "_", tt, "_", ii, " - ", var_u_p, " <= 0")
      c3 = paste0("andP_", ss, "_", tt, "_", ii, " - ", var_x_p, " <= 0")
      
      var_u_m <- variables[[ii]]$variables[variables[[ii]]$idxEdgesDown[jj]]
      var_x_m <- variables[[ii]]$variables[which(variables[[ii]]$exp==
                                                   paste0("SpeciesDown ", 
                                                          tt, 
                                                          " in experiment ", 
                                                          ii))]
      
      c4 = paste0("andM_", ss, "_", tt, "_", ii, " - ", 
                  var_u_m, " - ", var_x_m, " >= -1")
      c5 = paste0("andM_", ss, "_", tt, "_", ii, " - ", var_u_m, " <= 0")
      c6 = paste0("andM_", ss, "_", tt, "_", ii, " - ", var_x_m, " <= 0")
      
      constraint1 = c(constraint1, c(c1, c2, c3, c4, c5, c6))
      
    }
    
  }
  
  constraint2 = c()
  for(jj in 1:length(variables$`Reaction Variables`$Explanation)){
    
    for(ii in 1:(length(variables)-1)){
      
      ss <- 
        strsplit(x = strsplit(
          x = variables[[ii]]$exp[variables[[ii]]$idxEdges[jj]], split = " ", 
          fixed = TRUE)[[1]][2], split = "=", fixed = TRUE)[[1]][1]
      tt <- 
        strsplit(x = strsplit(
          x = variables[[ii]]$exp[variables[[ii]]$idxEdges[jj]], split = " ", 
          fixed = TRUE)[[1]][2], split = "=", fixed = TRUE)[[1]][2]
      
      c1 <- paste0(variables[[ii]]$variables[variables[[ii]]$idxEdges[jj]], 
                   " - andP_", ss, "_", tt, "_", ii, " - andM_", ss, "_", 
                   tt, "_", ii, " <= 0")
      c2 <- paste0(variables[[ii]]$variables[variables[[ii]]$idxEdges[jj]], 
                   " - andP_", ss, "_", tt, "_", ii, " >= 0")
      c3 <- paste0(variables[[ii]]$variables[variables[[ii]]$idxEdges[jj]], 
                   " - andM_", ss, "_", tt, "_", ii, " >= 0")
      
      constraint2 = c(constraint2, c(c1, c2, c3))
      
    }
    
  }
  
  constraint3 = c()
  for(jj in 1:length(variables$`Reaction Variables`$Explanation)){
    
    c1 = variables$`Reaction Variables`$Variables[jj]
    c2 = c()
    
    for(ii in 1:(length(variables)-1)){
      
      c1 = paste0(c1, " - ", 
                  variables[[ii]]$variables[variables[[ii]]$idxEdges[jj]])
      c2 = c(c2, paste0(variables$`Reaction Variables`$Variables[jj], " - ", 
                        variables[[ii]]$variables[variables[[ii]]$idxEdges[jj]], 
                        " >= ", 0))
      
    }
    
    c1 <- paste0(c1, " <= 0")
    constraint3 <- c(constraint3, c(c1, c2))
    
  }

  constraints = c(constraint1, constraint2, constraint3)
  
  return(constraints)
  
}