pwayGraph-class          package:pathRender          R Documentation

_C_l_a_s_s "_p_w_a_y_G_r_a_p_h" - _e_x_t_e_n_s_i_o_n _t_o _g_r_a_p_h_N_E_L _f_o_r _p_a_t_h_w_a_y _r_e_n_d_e_r_i_n_g

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

     extension to graphNEL for pathway rendering

_O_b_j_e_c_t_s _f_r_o_m _t_h_e _C_l_a_s_s:

     Objects can be created by calls of the form  'new("pwayGraph",
     nodes, edgeL, edgemode)'.

     There is a plot method that will work reasonably well if the
     plotting surface is big enough.

_S_l_o_t_s:


     '_p_w_a_y_S_o_u_r_c_e': Object of class '"character"' KEGG or BIOCARTA 

     '_n_o_d_e_s': Object of class '"vector"' pathway constituents in the
          native vocabulary 

     '_e_d_g_e_L': Object of class '"list"' constituent relations in the
          native vocabulary 

     '_e_d_g_e_m_o_d_e': Object of class '"character"' directed, typically 

     '_e_d_g_e_D_a_t_a': Object of class '"attrData"' relationship attributes 

     '_n_o_d_e_D_a_t_a': Object of class '"attrData"' node attributes 

     '_g_r_a_p_h_D_a_t_a': Object of class '"list"' this holds the special
          rendering attributes for edges and nodes, for nodes it seems
          particularly important to have fixedsize = FALSE

_E_x_t_e_n_d_s:

     Class 'graphNEL-class', directly. Class 'graph-class', by class
     "graphNEL", distance 2.

_M_e_t_h_o_d_s:


     _p_l_o_t 'signature(x = "pwayGraph")': renders the pathway 

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

     Vince Carey <stvjc@channing.harvard.edu>

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

     showClass("pwayGraph")
     G1 = graphcMAP("stresspathway")
     G1@graphData$nAttrs$labels[1:10]

