plotgenes               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 (_g_e_n_e) _p_r_o_j_e_c_t_i_o_n_s _f_r_o_m _P_C_A _o_r _C_O_A. _O_n_l_y _l_a_b_e_l _v_a_r_i_a_b_l_e_s _a_t _e_n_d_s _o_f _a_x_e_s

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

     Graph xy plot of variables but only label variables at ends of X
     and Y axes. Useful for graphing genes coordinates ($co) resulting
     from PCA or COA of microarray data.

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

     plotgenes(coord, nlab = 10, axis1 = 1, axis2 = 2, 
     genelabels = row.names(coord), boxes = TRUE, 
     colpoints = "black", ...)

_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

    nlab: Numeric. An integer indicating the number of variables at
          ends of axes to be labelled

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

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

genelabels: A vector of gene (variable) labels. Default is
          row.names(coord)

   boxes: A logical, indicating whether a box should be plotted
          surrounding each variable label. The default is TRUE.

colpoints: The colour of the points on the plot. The default is "black"

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

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

     'plotgenes' calls the function 'genes' which return an index of
     the "top" variables at the ends of the x and y axes. 

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

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

     An xy plot

_N_o_t_e:

     'plotgenes' plots variables using 's.var', which is a modified
     version  of 's.label'.

_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.ord<-ord(khan$train, classvec=khan$train.classes) 
     }
     par(mfrow=c(2,2))
     #s.var(khan.ord$co, col=as.numeric(khan$train.classes), clabel=0.8)
     plotgenes(khan.ord, colpoints="red")
     plotgenes(khan.ord, colpoints="red", genelabels=khan$annotation$Symbol)
     plotgenes(khan.ord, colpoints="gray", genelabels=khan$annotation$Symbol,boxes=FALSE)

