zoom                   package:ape                   R Documentation

_Z_o_o_m _o_n _a _P_o_r_t_i_o_n _o_f _a _P_h_y_l_o_g_e_n_y

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

     This function plots simultaneously a whole phylogenetic tree
     (supposedly large) and a portion of it.

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

     zoom(phy, focus, subtree = FALSE, col = rainbow, ...)

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

     phy: an object of class '"phylo"'.

   focus: a vector, either numeric or character, or a list of vectors
          specifying the tips to be focused on.

 subtree: a logical indicating whether to show the context of the
          extracted subtrees.

     col: a vector of colours used to show where the subtrees are in
          the main tree, or a function .

     ...: further arguments passed to 'plot.phylo'.

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

     This function aims at exploring very large trees. The main
     argument is a phylogenetic tree, and the second one is a vector or
     a list of vectors specifying the tips to be focused on. The
     vector(s) can be either numeric and thus taken as the indices of
     the tip labels, or character in which case it is taken as the
     corresponding tip labels.

     The whole tree is plotted on the left-hand side in a narrower
     sub-window (about a quarter of the device) without tip labels. The
     subtrees consisting of the tips in `focus' are extracted and
     plotted on the right-hand side starting from the top left corner
     and successively column-wise.

     If the argument `col' is a vector of colours, as many colours as
     the number of subtrees must be given. The alternative is to give a
     function that will create colours or grey levels from the number
     of subtrees: see 'rainbow' for some possibilities with colours.

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

     Emmanuel Paradis paradis@isem.univ-montp2.fr

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

     'plot.phylo', 'drop.tip', 'layout', 'rainbow', 'grey'

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

     ## Not run: 
     data(chiroptera)
     zoom(chiroptera, 1:20, subtree = TRUE)
     zoom(chiroptera, grep("Plecotus", chiroptera$tip.label))
     zoom(chiroptera, list(grep("Plecotus", chiroptera$tip.label),
                           grep("Pteropus", chiroptera$tip.label)))
     ## End(Not run)

