adding fixes that handle out-of-order clones and a test

R/draw.R

@@ -252,9 +252,14 @@ fishPlot <- function(fish,shape="polygon", vlines=NULL, col.vline="#FFFFFF99", v
   #(if neither is set, bg will just be white)
 
   ##draw the clusters one at a time, being sure that parents go before children
-  for(parent in sort(unique(fish@parents))){
-    for(i in which(fish@parents==parent)){
-
+  parentsList = 0
+  while(length(parentsList) > 0){
+    parent = parentsList[[1]]
+    children =  which(fish@parents==parent)
+    parentsList = parentsList[-1]
+    parentsList = c(parentsList, children)
+    numChildren = length(children)
+    for(i in children){
       pad.left=pad
       if(parent>0){
         pad.left=pad*0.4

R/layout.R

@@ -30,10 +30,14 @@ layoutClones <- function(fish,separate.independent.clones=FALSE){
     xpos = rep(timepoint, length(fish@parents))
 
     ##starting with those with no parents, then moving through each existing parent
-    for(parent in sort(unique(fish@parents))){
-
-      numChildren = length(fish@parents[fish@parents==parent])
-      spacing = 0
+    parentsList = 0
+    while(length(parentsList) > 0){
+        parent = parentsList[[1]]
+        children = which(fish@parents == parent)
+        parentsList = parentsList[-1]
+        parentsList = c(parentsList, children)
+        numChildren = length(children)
+        spacing = 0
       ##start at the bottom plus half the outer space
       y = fish@outer.space[timepos]/2;
 
@@ -54,7 +58,7 @@ layoutClones <- function(fish,separate.independent.clones=FALSE){
       }
 
       ##for each clone that has this parent, get coords
-      for(clone in which(fish@parents==parent)){
+      for(clone in children){
 
         ##clone absent, don't need to add positions
         if(fish@frac.table[clone,timepos] == 0){

README.md

@@ -93,4 +93,3 @@ A: The original visualization was put together by [Joshua McMichael](https://git
 
 ## Notes
 Citation: [Visualizing tumor evolution with the fishplot package for R](https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-016-3195-z). Miller CA, McMichael J, Dang HX, Maher CA, Ding L, Ley TJ, Mardis ER, Wilson RK. BMC Genomics. doi:10.1186/s12864-016-3195-z
-

tests/test.R

@@ -161,3 +161,29 @@ fishPlot(fish, shape="polygon", vlab=c("Primary","Post-AI"),
          cex.title=0.7, cex.vlab=0.8,ramp.angle=1, pad.left=0.3)
 
 dev <- dev.off()
+
+##-------------------------------------------
+## test if the clones are not listed in order
+## see https://github.com/chrisamiller/fishplot/pull/2
+pdf("ordertest.pdf", width=8, height=5)
+library(fishplot)
+    timepoints=c(0,30,75,150)
+    frac.table = matrix(
+        c(100, 45, 00, 00,
+          02, 00, 00, 00,
+          02, 00, 02, 01,
+          98, 00, 95, 40),
+        ncol=length(timepoints))
+    parents = c(0,1,1,3)
+
+  ##Now just rearrange clones.
+  frac.table = frac.table[c(4,3,2,1),]
+  parents = c(2,4,4,0)
+
+  fish = createFishObject(frac.table,parents,timepoints=timepoints)
+  fish = layoutClones(fish)
+  fishPlot(fish,shape="spline",title.btm="Sample1",
+           cex.title=0.5, vlines=c(0,150),
+           vlab=c("day 0","day 150"))
+dev <- dev.off()
+