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optsol_phppClass.R

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    Claus Jonathan Fritzemeier authored
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    optsol_phppClass.R 5.23 KiB
    #  optsol_phppClass.R
    #  FBA and friends with R.
    #
    #  Copyright (C) 2010-2014 Gabriel Gelius-Dietrich, Dpt. for Bioinformatics,
    #  Institute for Informatics, Heinrich-Heine-University, Duesseldorf, Germany.
    #  All right reserved.
    #  Email: geliudie@uni-duesseldorf.de
    #  
    #  This file is part of sybil.
    #
    #  Sybil is free software: you can redistribute it and/or modify
    #  it under the terms of the GNU General Public License as published by
    #  the Free Software Foundation, either version 3 of the License, or
    #  (at your option) any later version.
    #
    #  Sybil is distributed in the hope that it will be useful,
    #  but WITHOUT ANY WARRANTY; without even the implied warranty of
    #  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    #  GNU General Public License for more details.
    #
    #  You should have received a copy of the GNU General Public License
    #  along with sybil.  If not, see <http://www.gnu.org/licenses/>.
    
    
    # optsol_phppClass
    
    
    #------------------------------------------------------------------------------#
    #                   definition of the class optsol_phpp                        #
    #------------------------------------------------------------------------------#
    
    setClass("optsol_phpp",
             representation(
                  ctrlflm  = "matrix",   # fixed flux values of control reactions
                  redCosts = "matrix"    # reduced costs
             ),
             contains = "optsol_robAna"
    )
    
    
    #------------------------------------------------------------------------------#
    #                            setters and getters                               #
    #------------------------------------------------------------------------------#
    
    
    # ctrlfl
    setMethod("ctrlfl", signature(object = "optsol_phpp"),
              function(object) {
                  return(object@ctrlflm)
              }
    )
    
    setReplaceMethod("ctrlfl", signature = (object = "optsol_phpp"),
                     function(object, value) {
                         object@ctrlflm <- value
                         return(object)
                     }
    )
    
    
    # redCost
    setMethod("getRedCosts", signature(lp = "optsol_phpp"),
              function(lp) {
                  return(lp@redCosts)
              }
    )
    
    
    #------------------------------------------------------------------------------#
    #                               other methods                                  #
    #------------------------------------------------------------------------------#
    
    setMethod("plot", signature(x = "optsol_phpp", y = "missing"),
              function(x, y,
                       xlab = list(label = react_id(ctrlr(x)[1]),
                                   rot = 30,
                                   cex = 0.8),
                       ylab = list(label = react_id(ctrlr(x)[2]),
                                   rot = -40,
                                   cex = 0.8),
                       zlab = list(label = obj_func(x),
                                   rot = 90,
                                   cex = 0.8),
                       scales = list(arrows = FALSE,
                                     cex = 0.6,
                                     font = 3,
                                     tck = 1,
                                     col = "black"),
                       par.settings = list(axis.line = list(col = "transparent")),
                       shade = TRUE,
                       shade.colors = function(irr, ref, height, w = 0.75) {
                                 grey(w * irr + (1 - w) * (1-(1-ref)^0.75)) },
                       ...) {
    
                  pic <- wireframe(lp_obj(x) ~ ctrlfl(x)[,1] * ctrlfl(x)[,2],
                                   scales = scales,
                                   shade = shade,
                                   par.settings = par.settings,
                                   shade.colors = shade.colors,
                                   xlab = xlab, ylab = ylab, zlab = zlab, ...)
                  return(pic)
    
              }
    )
    
    #------------------------------------------------------------------------------#
    
    
    # value for col.regions are the Greys from RColorBrewer:
    # brewer.pal(9, "Greys")
    # c("#FFFFFF", "#F0F0F0", "#D9D9D9", "#BDBDBD", "#969696", "#737373",
    #   "#525252", "#252525", "#000000")
    
    setMethod("plot", signature(x = "optsol_phpp", y = "character"),
              function(x, y, #rcbp = "Greys",
                       main = paste("Reduced Costs:", y),
                       xlab = react_id(ctrlr(x)[1]),
                       ylab = react_id(ctrlr(x)[2]),
                       shrink = c(0.95, 0.95),
                       #col.regions = colorRampPalette(brewer.pal(brewer.pal.info[rcbp, ][["maxcolors"]], rcbp))(100),
                       col.regions = colorRampPalette(c("#FFFFFF", "#F0F0F0",
                                        "#D9D9D9", "#BDBDBD", "#969696", "#737373",
                                        "#525252", "#252525", "#000000"))(100),
                       ...) {
    
                  if (any(is.na(getRedCosts(x)))) {
                      warning("solution object does not contain reduced costs")
                      pic <- NA
                  }
                  else {
                      pic <- levelplot(
                          getRedCosts(x)[ ,y] ~ ctrlfl(x)[,1] * ctrlfl(x)[,2],
                          xlab = xlab,
                          ylab = ylab,
                          main = main,
                          col.regions = col.regions,
                          shrink = shrink, ...)
                  }
                  return(pic)
              }
    )