--- a
+++ b/R/part01.R
@@ -0,0 +1,156 @@
+################################################################################
+# 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)
+}
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