plotarrays               package:made4               R Documentation

_G_r_a_p_h _x_y _p_l_o_t _o_f _v_a_r_i_a_b_l_e (_a_r_r_a_y) _p_r_o_j_e_c_t_i_o_n_s _f_r_o_m _o_r_d_i_n_a_t_i_o_n, _b_e_t_w_e_e_n _g_r_o_u_p _a_n_a_l_y_s_i_s _o_r _c_o_i_n_e_r_t_i_a _a_n_a_l_y_s_i_s.

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

     Graph xy plot of variables using s.var, s.groups or s.match.col.
     Useful for visualising array coordinates ($li) resulting from ord,
     bga or cia of microarray data.

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

     plotarrays(coord, axis1 = 1, axis2 = 2, arraylabels = NULL, classvec=NULL,  graph = c("groups", "simple", "labels", "groups2", "coinertia","coinertia2"), labelsize=1, star=1, ellipse=1, ...)

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

   coord: a 'data.frame' or 'matrix' or object from 'ord' 'bga' or
          'cia' analysis with at least two columns, containing x, y
          coordinates to be plotted

   axis1: An integer, the column number for the x-axis. Default is 1,
          so axes 1 is dudivar[,1]

   axis2: An integer, the column number for the y-axis. Default is 2, 
          so axes 2 is dudivar[,2]

arraylabels: A vector of variables labels. Default is row.names(coord)

classvec: A 'factor' or 'vector' which describes the classes in
          'coord'.  Default is NULL. If included variables will be
          coloured by class.

   graph: A character of type  "groups", "simple", "labels", "groups2",
          "coinertia" or "coinertia2" which specifies the type of plot
          type or "graph" to be drawn. By default the  graph will be
          selected depending on the class of cooord, and whether a
          classvector is specified

labelsize: 

    star: If drawing groups, whether to join samples to centroid
          creating a "star"

 ellipse: If drawing groups, whether to draw an ellipse or ring around
          the samples

     ...: further arguments passed to or from other method 

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

     'plotarrays' calls the function 's.var', 's.groups' or
     's.match.col'.

     If you wish to return a table or list of the top array at the end
     of an axis, use the function 'topgenes'.

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

     An xy plot

_N_o_t_e:

     'plotarrays' plots variables using 's.var', 's.groups',
     's.match.col' which are modifieds version of 's.label', 's.class'.
     , and 's.match'.

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

     Aedin Culhane

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

     See Also as 's.var' and 's.label'

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

     data(khan)
     if (require(ade4, quiet = TRUE)) {
     khan.bga<-bga(khan$train, khan$train.classes) 
     }
     attach(khan.bga)
     par(mfrow=c(2,1))
     plotarrays(khan.bga)
     plotarrays(khan.bga, graph="simple")
     plotarrays(khan.bga, graph="labels")
     plotarrays(khan.bga, graph="groups")
     plotarrays(khan.bga, graph="groups2")

