few corrections and fixes

[ape.git] / R / scales.R

diff --git a/R/scales.R b/R/scales.R
index c8da7e79ec54692c272fcd7a1851ca5293cf1bb6..2243278b19e8b94c9c6b6e652c32687eb39f9a92 100644 (file)
--- a/R/scales.R
+++ b/R/scales.R
@@ -1,24 +1,75 @@
-## scales.R (2008-02-28)
+## scales.R (2009-12-16)
 
 ##   Add a Scale Bar or Axis to a Phylogeny Plot
 
 ## add.scale.bar: add a scale bar to a phylogeny plot
 ## axisPhylo: add a scale axis on the side of a phylogeny plot
 
-## Copyright 2002-2008 Emmanuel Paradis
+## Copyright 2002-2009 Emmanuel Paradis
 
 ## This file is part of the R-package `ape'.
 ## See the file ../COPYING for licensing issues.
 
-add.scale.bar <- function(x = 0, y = 1, length = NULL, ...)
+add.scale.bar <- function(x, y, length = NULL, ask = FALSE, ...)
 {
     lastPP <- get("last_plot.phylo", envir = .PlotPhyloEnv)
+    direc <- lastPP$direction
     if (is.null(length)) {
-        nb.digit <- ceiling(log10(mean(lastPP$xx))) - 2
+        nb.digit <-
+          if (direc %in% c("rightwards", "leftwards")) diff(range(lastPP$xx))
+          else diff(range(lastPP$yy))
+        nb.digit <- ceiling(log10(nb.digit)) - 2
         length <- eval(parse(text = paste("1e", nb.digit, sep = "")))
     }
-    segments(x, y, x + length, y)
-    text(x + length * 1.1, y, as.character(length), adj = c(0, 0.5), ...)
+
+    if (ask) {
+        cat("\nClick where you want to draw the bar\n")
+        x <- unlist(locator(1))
+        y <- x[2]
+        x <- x[1]
+    } else if (missing(x) || missing(y)) {
+        if (lastPP$type %in% c("phylogram", "cladogram")) {
+            switch(direc,
+                   "rightwards" = {
+                       x <- 0
+                       y <- 1
+                   },
+                   "leftwards" = {
+                       x <- max(lastPP$xx)
+                       y <- 1
+                   },
+                   "upwards" = {
+                       x <- max(lastPP$xx)
+                       y <- 0
+                   },
+                   "downwards" = {
+                       x <- 1
+                       y <- max(lastPP$yy)
+                   })
+        } else {
+            direc <- "rightwards" # just to be sure for below
+            x <- lastPP$x.lim[1]
+            y <- lastPP$y.lim[1]
+        }
+    }
+
+    switch(direc,
+           "rightwards" = {
+               segments(x, y, x + length, y)
+               text(x + length * 1.1, y, as.character(length), adj = c(0, 0.5), ...)
+           },
+           "leftwards" = {
+               segments(x - length, y, x, y)
+               text(x - length * 1.1, y, as.character(length), adj = c(1, 0.5), ...)
+           },
+           "upwards" = {
+               segments(x, y, x, y + length)
+               text(x, y + length * 1.1, as.character(length), adj = c(0, 0.5), srt = 90, ...)
+           },
+           "downwards" = {
+               segments(x, y - length, x, y)
+               text(x, y - length * 1.1, as.character(length), adj = c(0, 0.5), srt = 270, ...)
+           })
 }
 
 axisPhylo <- function(side = 1, ...)