changed y-xis order to help with legend AND made fossisl obey arg "li…

…neageColors"
brpetrucci · Aug 25, 2023 · 83056a3 · 83056a3
1 parent 419fa5d
commit 83056a3
Showing 1 changed file with 7 additions and 2 deletions.
diff --git a/R/draw.sim.R b/R/draw.sim.R
@@ -340,7 +340,7 @@ draw.sim <- function (sim, traits = NULL, fossils = NULL, lineageColors = NULL,
 
  # limits in y axis
  if (!("ylim" %in% names(args))) {
- formals(plot.default)$ylim <- c(0, (length(sim$TE) + 1))
+ formals(plot.default)$ylim <- c((length(sim$TE) + 1),0)
  }
 
  # no frame
@@ -582,9 +582,14 @@ draw.sim <- function (sim, traits = NULL, fossils = NULL, lineageColors = NULL,
 
  # and get their colors
  colFossils <- traitColors[unlist(traitSummary[traitID]) + 1] 
- } else {
+ } else if(is.null(lineageColors)){
  # otherwise, all red
  colFossils <- rep("red", times = length(sim$TE))
+ }else{
+ if(length(lineageColors)!=length(sim$TE)){
+ stop("\"lineageColors\" and sim do not match. See \"draw.sim\" help page.")
+ }
+ colFossils <- lineageColors[as.numeric(sub("t","", fossils$Species))]
  }
 
  # check which fossils to draw