orditorp                package:vegan                R Documentation

_A_d_d _T_e_x_t _o_r _P_o_i_n_t_s _t_o _O_r_d_i_n_a_t_i_o_n _P_l_o_t_s

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

     The function adds 'text' or 'points' to ordination plots.  Text
     will be used if this can be done without overwriting other text
     labels, and points will be used otherwise. The function can help
     in reducing clutter in ordination graphics, but manual editing may
     still be necessary.

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

     orditorp(x, display, labels, choices = c(1, 2), priority, tcex = 0.7,
         pcex, tcol = par("col"), pcol, pch = par("pch"), air = 1, ...)

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

       x: A result object from ordination or an 'ordiplot' result. 

 display: Items to be displayed in the plot.  Only one alternative is
          allowed. Typically this is '"sites"' or '"species"'.  

  labels: Optional text used for labels. Row names will be used if this
          is missing. 

 choices: Axes shown.

priority: Text will be used for items with higher priority if labels
          overlap.  This should be vector of the same length as the
          number of items plotted.

tcex, pcex: Text and point sizes, see 'plot.default'..

tcol, pcol: Text and point colours, see 'plot.default'.

     pch: Plotting character, see 'points'.

     air: Amount of empty space between text labels. Values <1 allow
          overlapping text.

     ...: Other arguments to 'text' and 'points'.  

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

     Function 'orditorp' will add either text or points to an existing
     plot. The items with high 'priority' will be added first and
     'text' will be used if this can be done without overwriting
     previous labels,and 'points' will be used otherwise. If 'priority'
     is missing, labels will be added from the outskirts to the centre.
     Function 'orditorp' can be used with most ordination results, or
     plotting results from 'ordiplot' or ordination plot functions
     ('plot.cca', 'plot.decorana', 'plot.metaMDS').

_V_a_l_u_e:

     The function returns invisibly a logical vector where 'TRUE' means
     that item was labelled with text and 'FALSE' means that it was
     marked with a point. The returned vector can be used as the
     'select' argument in ordination 'text' and 'points' functions.

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

     Jari Oksanen

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

     ## A cluttered ordination plot :
     data(BCI)
     mod <- cca(BCI)
     plot(mod, dis="sp", type="t")
     # Now with orditorp and abbreviated species names
     cnam <- make.cepnames(names(BCI))
     plot(mod, dis="sp", type="n")
     stems <- colSums(BCI)
     orditorp(mod, "sp", label = cnam, priority=stems, pch="+", pcol="grey")

