################################################################################

# Function which plots the drug characteristics

################################################################################

plotPathways = function(dat) {

  # quiets concerns of R CMD check "no visible binding for global variable"

  Pathway=NULL; No=NULL; Group=NULL

  ordM = sort(table(dat$group), decreasing=TRUE)

  ordS = tapply(dat$"target_category", dat$group, function(pth) {

    sort(table(pth), decreasing=TRUE)

  })

  ocur  = ordS[names(ordM)]

  # transform the list to LF df

  tmp = do.call(rbind, lapply(names(ocur), function(pathgroup) {

    data.frame(Group=pathgroup,

               Pathway=names(ocur[[pathgroup]]),

               No=as.vector(unname(ocur[[pathgroup]])))

  }))

  tmp$Group = factor(tmp$Group, levels=rev(names(ocur)))

  # order the targets by occurance and leave Other last

  lev = sort(tapply(tmp$No, tmp$Pathway, function(x) sum(x)), decreasing=TRUE)

  lev = c(lev[-which(names(lev)=="Other")], lev["Other"])

  tmp$Pathway = factor(tmp$Pathway, levels=names(lev))

  # range to be plotted on the x axis

  widthmax = max(lev)+1

  g = ggplot(tmp, aes(x=Pathway, y=No, fill=Group)) +

    geom_bar(width=0.6, stat="identity") +

    theme_bw() + scale_fill_manual(values=typeColor, name="Drug type") +

    scale_y_continuous(breaks=seq(0,20,2), expand = c(0,0),

                       limits = c(0,widthmax)) +

    xlab("") + ylab("Number of drugs") +

    theme(axis.text.x=element_text(size=12, angle = 45, vjust = 1, hjust=1),

          axis.text.y=element_text(size=12), axis.title.y=element_text(size=12),

          legend.text=element_text(size=12), legend.title=element_text(size=12))

  # make gtable

  hghts = c(0.2,0.22*widthmax,1.7)

  wdths = c(1,0.3,0.2,0.26*length(levels(tmp$Pathway)),0.1)

  gg = ggplotGrob(g)

  gt = gtable(widths=unit(wdths, "in"), heights=unit(hghts, "in"))

  # fill in the gtable

  gt = gtable_add_grob(gt, gtable_filter(gg, "panel"), 2, 4) # panel

  gt = gtable_add_grob(gt, gg$grobs[[whichInGrob(gg, "axis-b")]], 3, 4) # x axis

  gt = gtable_add_grob(gt, gg$grobs[[whichInGrob(gg, "axis-l")]], 2, 3) # y axis

  gt = gtable_add_grob(gt, gg$grobs[[whichInGrob(gg, "ylab-l")]], 2, 2)

  # make legend

  wdthsl = c(2)

  hghtsl = c(1.5)

  gtl = gtable(widths=unit(wdthsl, "in"), heights=unit(hghtsl, "in"))

  gtl = gtable_add_grob(gtl, gg$grobs[[whichInGrob(gg, "guide-box-right")]], 1, 1)

  return(list("figure"=list(width=sum(wdths), height=sum(hghts), plot=gt),

              "legend"=list(width=sum(wdthsl), height=sum(hghtsl), plot=gtl)))

}

################################################################################

# Function which plots the patient characteristics as a bar plot

################################################################################

plotPatientStat = function(pats, gap, ptab=BloodCancerMultiOmics2017::patmeta) {

  # quiets concerns of R CMD check "no visible binding for global variable"

  Diagnosis=NULL; NO=NULL; Origin=NULL

  # create plotting data.frame with Diagnosis, Origin and number of cases 

  plotDF = data.frame(table(ptab[pats,"Diagnosis"]))

  colnames(plotDF) = c("Diagnosis","NO")

  plotDF$Diagnosis = as.character(plotDF$Diagnosis)

  plotDF$Origin = 

    names(diagAmt)[unlist(sapply(plotDF$Diagnosis,

                                        function(x) grep(x, diagAmt)))]

  # set the order of Diagnosis

  ord = smunlist(

    tapply(1:nrow(plotDF), plotDF$Origin,

           function(idx) plotDF$Diagnosis[idx[order(plotDF[idx,"NO"], 

           decreasing=TRUE)]])[names(diagAmt)])

  plotDF$Diagnosis = factor(plotDF$Diagnosis, levels=ord)

  # adjustments for gap

  if(any(plotDF$NO>gap[1] & plotDF$NO<gap[2]))

    stop("Gap is wrongly defined")

  idx = plotDF$NO > gap[2]

  plotDF$NO[idx] = plotDF$NO[idx] - (gap[2]-gap[1])

  # round the ceiling to tens (find the latest break point)

  xlimits = c(0, moround(max(plotDF$NO),5)) 

  xbreaks = seq(0, xlimits[2], 10)

  # labels for breaks

  xlabels = ifelse(xbreaks>gap[1], xbreaks + (gap[2]-gap[1]), xbreaks)

  g = ggplot() + geom_bar(data=plotDF, aes(x=Diagnosis, y=NO, fill=Origin),

                          stat="identity", colour="black", size=0.1, width=.5) +

    theme_bw() + scale_x_discrete() +

    scale_fill_manual(values=colDiagL) +

    scale_y_continuous(breaks=xbreaks, labels=xlabels, expand=c(0,0),

                       limits=xlimits) +

    geom_hline(yintercept=c(gap[1]+5,gap[1]+5.5), linetype="dashed", size=0.3) +

    xlab("") + ylab("") +

    theme(axis.text.x=element_text(size=12, angle=45, hjust=1),

          axis.text.y=element_text(size=12),

          legend.text=element_text(size=12),

          legend.title=element_text(size=12),

          legend.key.size=unit(0.2,"in"),

          legend.title.align=0.5, legend.text.align=0,

          panel.border=element_rect(color="black", size=0.1))

  # construct the gtable

  wdths = c(0.4, 0.4*length(levels(plotDF$Diagnosis)), 0.1) 

  hghts = c(0.2, 0.04*max(xbreaks), 1)

  gt = gtable(widths=unit(wdths, "in"), heights=unit(hghts, "in"))

  ## make grobs

  gg = ggplotGrob(g)

  ## fill in the gtable

  gt = gtable_add_grob(gt, gtable_filter(gg, "panel"), 2, 2)

  gt = gtable_add_grob(gt, gg$grobs[[whichInGrob(gg, "axis-l")]], 2, 1) # y axis

  gt = gtable_add_grob(gt, gg$grobs[[whichInGrob(gg, "axis-b")]], 3, 2) # x axis

  # make legend

  wdthsl = c(2)

  hghtsl = c(1.5)

  gtl = gtable(widths=unit(wdthsl, "in"), heights=unit(hghtsl, "in"))

  gtl = gtable_add_grob(gtl, gg$grobs[[whichInGrob(gg, "guide-box-right")]], 1, 1)

  return(list("figure"=list(width=sum(wdths), height=sum(hghts), plot=gt),

              "legend"=list(width=sum(wdthsl), height=sum(hghtsl), plot=gtl)))

}

################################################################################

# Function which plots the legends in one row

################################################################################

drawLegends = function(plobj, lng=5, w=2, h=2) { #, alone=FALSE

  gt = gtable(widths=unit(rep(w, lng), "in"), heights=unit(h, "in"))

  plotlen = length(plobj)

  if(plotlen>lng)

    stop("Number of objects to plot exceeds the number of available slots!")

  for(po in 1:plotlen) {

    gt = gtable_add_grob(gt,

                         plobj[[po]]$grobs[[whichInGrob(plobj[[po]],

                                                        "guide-box-right")]], 1, po)

  }

  grid.draw(gt)

}