Plot.all            package:GlobalAncova            R Documentation

_C_o_m_b_i_n_e_d _v_i_s_u_a_l_i_z_a_t_i_o_n _o_f _s_e_q_u_e_n_t_i_a_l _d_e_c_o_m_p_o_s_i_t_i_o_n _a_n_d _i_n_f_l_u_e_n_c_e _o_f _s_i_n_g_l_e _g_e_n_e_s _o_n _t_h_e _G_l_o_b_a_l_A_n_c_o_v_a _s_t_a_t_i_s_t_i_c

_D_e_s_c_r_i_p_t_i_o_n:

     Plot that combines 'Plot.genes' and 'Plot.sequential' into one
     graphic.

_U_s_a_g_e:

     Plot.all(xx, formula, model.dat = NULL, test.genes = NULL, name.geneset = "")

_A_r_g_u_m_e_n_t_s:

      xx: Matrix of gene expression data, where columns correspond to
          samples and rows to genes. The data should be properly
          normalized beforehand (and log- or otherwise transformed).
          Missing values are not allowed. Gene and sample names can be
          included as the row and column names of 'xx'.

 formula: Model formula for the linear model.

model.dat: Data frame that contains all the variable information for
          each sample.

test.genes: Vector of gene names or gene indices specifying a gene set.

name.geneset: Name of the plotted geneset.

_N_o_t_e:

     This work was supported by the NGFN project 01 GR 0459, BMBF,
     Germany.

_A_u_t_h_o_r(_s):

     Ramona Scheufele ramona.scheufele@charite.de 
      Reinhard Meister meister@tfh-berlin.de
      Manuela Hummel hummel@ibe.med.uni-muenchen.de 
      Urlich Mansmann mansmann@ibe.med.uni-muenchen.de

_S_e_e _A_l_s_o:

     'Plot.genes', 'Plot.sequential', 'GlobalAncova.decomp',
     'GlobalAncova'

_E_x_a_m_p_l_e_s:

     data(vantVeer)
     data(phenodata)
     data(pathways)

     Plot.all(vantVeer, formula = ~ ERstatus + metastases + grade, model.dat = phenodata, test.genes = pathways[[3]], name.geneset = "cell cycle pathway")

