nodelabels                package:ape                R Documentation

_L_a_b_e_l_l_i_n_g _t_h_e _N_o_d_e_s _o_f _a _T_r_e_e

_D_e_s_c_r_i_p_t_i_o_n:

     This function adds labels to or near the nodes of a tree using
     text or plotting symbols. The text can be framed.

_U_s_a_g_e:

     nodelabels(text, node, adj = c(0.5, 0.5), frame = "rect",
                pch = NULL, col = "black", bg = "lightblue", ...)

_A_r_g_u_m_e_n_t_s:

    text: a vector of mode character giving the text to be printed. Can
          be left empty.

    node: a vector of mode numeric giving the numbers of the nodes
          where the text or the symbols are to be printed. Can be left
          empty.

     adj: one or two numeric values specifying the horizontal and
          vertical, respectively, justification of the text. By
          default, the text is centered horizontally and vertically. If
          a single value is given, this alters only the horizontal
          position of the text.

   frame: a character string specifying the kind of frame to be printed
          around the text. This must be one of "rect" (the default),
          "circle", "none", or any unambiguous abbreviation of these.

     pch: a numeric giving the type of plotting symbol to be used; this
          is eventually recycled. See 'par' for R's plotting symbols.
          If 'pch' is used, then 'text' is ignored.

     col: a character string giving the color to be used for the
          plotting symbols; this is eventually recycled.

      bg: a character string giving the color to be used for the
          background of the text frames or of the plotting symbols if
          it applies; this is eventually recycled.

     ...: further arguments passed to the 'text' or 'points' functions
          (e.g. 'cex' to alter the size of the text or the symbols, or
          'font' for the text; see the examples below).

_D_e_t_a_i_l_s:

     If the arguments 'text' is missing and 'pch' is left as 'NULL',
     then the numbers of the nodes are printed.

     If 'node' is missing, then the text or the symbols are printed on
     all nodes.

     A simple call of the function with no arguments (i.e.
     'nodelabels()') prints the numbers of all nodes.

_A_u_t_h_o_r(_s):

     Emmanuel Paradis paradis@isem.univ-montp2.fr

_S_e_e _A_l_s_o:

     'plot.phylo'

_E_x_a_m_p_l_e_s:

     tr <- read.tree(text = "((Homo,Pan),Gorilla);")
     plot(tr)
     nodelabels("7.3 Ma", 1, frame = "r", bg = "yellow", adj = 0)
     nodelabels("5.4 Ma", 2, frame = "c", bg = "tomato", font = 3)

     data(bird.orders)
     plot(bird.orders, use.edge.length = FALSE, font = 1)
     bs <- round(runif(22, 90, 100), 0) # some imaginary bootstrap values
     bs2 <- round(runif(22, 90, 100), 0)
     bs3 <- round(runif(22, 90, 100), 0)
     nodelabels(bs, adj = 1.2)
     nodelabels(bs2, adj = -0.2, bg = "yellow")

     ### something more classical
     plot(bird.orders, use.edge.length = FALSE, font = 1)
     nodelabels(bs, adj = -0.2, frame = "n", cex = 0.8)
     nodelabels(bs2, adj = c(1.2, 1), frame = "n", cex = 0.8)
     nodelabels(bs3, adj = c(1.2, -0.2), frame = "n", cex = 0.8)

     ### the same but we play with the font
     plot(bird.orders, use.edge.length = FALSE, font = 1)
     nodelabels(bs, adj = -0.2, frame = "n", cex = 0.8, font = 2)
     nodelabels(bs2, adj = c(1.2, 1), frame = "n", cex = 0.8, font = 3)
     nodelabels(bs3, adj = c(1.2, -0.2), frame = "n", cex = 0.8)

     plot(bird.orders, "u", FALSE, font = 1, lab4ut = "a")
     nodelabels(cex = .75, bg = "yellow")

