# MvA plotting for microarray data


# Copyright 2003 By Don Armstrong

# This program 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 2 of the License, or
# (at your option) any later version.

# This program 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 this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA
# 02111-1307, USA.

# $Id: mva_plotting.R,v 1.5 2006/06/10 04:14:45 don Exp $


library("grid")
library("ggplot2")

# mva.plot
# Plots a pairwise M versus A plot with a loess fit line
##' Plots a pairwise M versus A plot with a loess fit line
##'
##' .. content for \details{} ..
##' @title mva.plot.pair
##' @param array Array of data to plot
##' @param title Title of plot (Default: FALSE; no title)
##' @param small.positive replace numbers less than 0 with this
##' @author Don Armstrong \email{don@@donarmstrong.com}
mva.plot.pair <- function(array,title=FALSE,small.positive=0.1){
  size <- ncol(array)
  npair <- size*(size-1)/2
  height <- min(round((npair*3/4)^0.5),3)
  width <- min(ceiling(npair/height),3)
  def.par <- par(no.readonly = TRUE)
  mva.layout <- grid.layout(ncol=width,nrow=height)
  pushViewport(viewport(layout=mva.layout))
  ## we could also use combn here instead
  num.plot <- 0
  for(a in 1:(size-1)){
      for(b in (a+1):size){
          num.plot <- num.plot + 1
          group.1 <- array[,a]
          group.2 <- array[,b]
          group.keep <- is.finite(group.1) & is.finite(group.2)
          group.1 <- group.1[group.keep]
          group.2 <- group.2[group.keep]
          group.min <- min(c(group.1,group.2))
          if (group.min <= 0) {
              group.1 <- group.1 - group.min + small.positive
              group.2 <- group.2 - group.min + small.positive
          }
          A <- 0.5*log2(group.1*group.2)
          M <- log2(group.1/group.2)
          temp.frame <- na.omit(data.frame(cbind(A,M)))
          if (num.plot > 1 &&
              floor((num.plot -1)/ width) %% height == 0 &&
              (num.plot-1) %% width == 0) {
              popViewport(1)
              grid.text(title,x=unit(0.0,"npc")+unit(1,"lines"),y=unit(0.5,"npc"),just="center",rot=90)
              grid.newpage()
              pushViewport(viewport(layout=mva.layout))
          }
          ## print(floor((num.plot -1)/ width) %% height+1)
          ## print((num.plot - 1)%% width+1)
          print(ggplot(temp.frame,aes(y=M,x=A))+
                geom_hex()+
                stat_smooth(method="gam")+
                ggtitle(paste0(colnames(array)[a],"\nvs\n",colnames(array)[b]))+
                theme(legend.position="none"),
                vp=viewport(layout.pos.row=floor((num.plot -1)/ width) %% height+1, layout.pos.col=((num.plot - 1)%% width+1)))
                
      }
  }
  popViewport()
}