various corrections

[ape.git] / R / cophyloplot.R

diff --git a/R/cophyloplot.R b/R/cophyloplot.R
index 04425c64360aa171f399fb78b790c5d444bfce06..faf9e34ae792f5571dc4b80910e4514c27b3b719 100644 (file)
--- a/R/cophyloplot.R
+++ b/R/cophyloplot.R
@@ -53,7 +53,7 @@ plotCophylo2 <-
               font = font, ...)
 {
     res <- list()
-###choice of the minimum space between the trees###
+###choice of the minimum space between the trees
     left <- max(nchar(x$tip.label, type = "width")) + length.line
     right <- max(nchar(y$tip.label, type = "width")) + length.line
     space.min <- left + right + gap * 2
@@ -66,8 +66,8 @@ plotCophylo2 <-
     res$a <- a
     b <- plotPhyloCoor(y, use.edge.length = use.edge.length,
                        direction = "leftwards", type = type)
- ###for the two trees to have the extreme leaves at the same ordinate.
-   a[, 2] <- a[, 2] - min(a[, 2])
+###for the two trees to have the extreme leaves at the same ordinate.
+    a[, 2] <- a[, 2] - min(a[, 2])
     b[, 2] <- b[, 2] - min(b[, 2])
     res$b <- b
     b2 <- b
@@ -122,9 +122,10 @@ plotCophylo2 <-
         }
     }
     if (show.tip.label) {
-        text(a[1:N.tip.x, ], cex = 0, font = font, pos = 4, labels = x$tip.label)
+        text(a[1:N.tip.x, ], cex = 0, font = font, pos = 4,
+             labels = x$tip.label)
         text(b2[1:N.tip.y, ], cex = 1, font = font, pos = 2,
-            labels = y$tip.label)
+             labels = y$tip.label)
     }
 ###links between associated taxa. Takes into account the size of the character strings of the taxa names.
     lsa <- 1:N.tip.x
@@ -142,26 +143,36 @@ plotCophylo2 <-
     else if (length(lwd)>=nrow(assoc)) lwidths<-lwd
     else  lwidths<-c(rep(lwd, as.integer(nrow(assoc)/length(lwd))+1))
 
-     #lty
+    #lty
     if (length(lty) == 1) ltype <- c(rep(lty, nrow(assoc)))
     else if (length(lty) >= nrow(assoc)) ltype <- lty
     else  ltype <- c(rep(lty, as.integer(nrow(assoc)/length(lty))+1))
 
     for (i in 1:nrow(assoc)) {
-
-      if (show.tip.label) {
-            decx[i] <- strwidth(x$tip.label[lsa[x$tip.label ==
-                assoc[i, 1]]])
-            decy[i] <- strwidth(y$tip.label[lsb[y$tip.label ==
-                assoc[i, 2]]])
-        }
-        else {
+        if (show.tip.label) {
+            decx[i] <- strwidth(x$tip.label[lsa[x$tip.label == assoc[i, 1]]])
+            decy[i] <- strwidth(y$tip.label[lsb[y$tip.label == assoc[i, 2]]])
+        } else {
             decx[i] <- decy[i] <- 0
         }
 
-        segments(a[lsa[x$tip.label == assoc[i, 1]], 1] + decx[i] +  gap, a[lsa[x$tip.label == assoc[i, 1]], 2], a[lsa[x$tip.label ==  assoc[i, 1]], 1] + gap + left, a[lsa[x$tip.label ==  assoc[i, 1]], 2], col = colors[i], lwd=lwidths[i], lty=ltype[i])
-        segments(b2[lsb[y$tip.label == assoc[i, 2]], 1] - (decy[i] +  gap), b2[lsb[y$tip.label == assoc[i, 2]], 2], b2[lsb[y$tip.label ==  assoc[i, 2]], 1] - (gap + right), b2[lsb[y$tip.label ==  assoc[i, 2]], 2], col = colors[i], lwd=lwidths[i], lty=ltype[i])
-        segments(a[lsa[x$tip.label == assoc[i, 1]], 1] + gap +  left, a[lsa[x$tip.label == assoc[i, 1]], 2], b2[lsb[y$tip.label ==  assoc[i, 2]], 1] - (gap + right), b2[lsb[y$tip.label == assoc[i, 2]], 2], col = colors[i], lwd=lwidths[i], lty=ltype[i])
+        segments(a[lsa[x$tip.label == assoc[i, 1]], 1] + decx[i] + gap,
+                 a[lsa[x$tip.label == assoc[i, 1]], 2],
+                 a[lsa[x$tip.label == assoc[i, 1]], 1] + gap + left,
+                 a[lsa[x$tip.label ==  assoc[i, 1]], 2],
+                 col = colors[i], lwd = lwidths[i], lty = ltype[i])
+
+        segments(b2[lsb[y$tip.label == assoc[i, 2]], 1] - (decy[i] + gap),
+                 b2[lsb[y$tip.label == assoc[i, 2]], 2],
+                 b2[lsb[y$tip.label == assoc[i, 2]], 1] - (gap + right),
+                 b2[lsb[y$tip.label ==  assoc[i, 2]], 2],
+                 col = colors[i], lwd = lwidths[i], lty = ltype[i])
+
+        segments(a[lsa[x$tip.label == assoc[i, 1]], 1] + gap + left,
+                 a[lsa[x$tip.label == assoc[i, 1]], 2],
+                 b2[lsb[y$tip.label == assoc[i, 2]], 1] - (gap + right),
+                 b2[lsb[y$tip.label == assoc[i, 2]], 2],
+                 col = colors[i], lwd = lwidths[i], lty = ltype[i])
     }
     if (return == TRUE)  return(res)
 }