maDefaultPar             package:marray             R Documentation

_D_e_f_a_u_l_t _g_r_a_p_h_i_c_a_l _p_a_r_a_m_e_t_e_r_s _f_o_r _m_i_c_r_o_a_r_r_a_y _o_b_j_e_c_t_s

_D_e_s_c_r_i_p_t_i_o_n:

     This function returns default graphical parameters for microarray
     objects. The parameters may be passed as arguments to the
     functions 'maBoxplot' and 'maPlot'.

_U_s_a_g_e:

     maDefaultPar(m, x, y, z)

_A_r_g_u_m_e_n_t_s:

       m: Microarray object of class '"marrayRaw"' and '"marrayNorm"'.

       x: Name of accessor method for the abscissa spot statistic,
          typically a slot name for the microarray object 'm', such as
          'maA'.

       y: Name of accessor method for the ordinate spot statistic,
          typically a slot name for the microarray object 'm', such as
          'maM'.

       z: Name of accessor method for the spot statistic used to
          stratify the data, typically a slot name for the microarray
          layout object (see '"marrayLayout"') such as 'maPlate' or a
          method such as 'maPrintTip'.

_V_a_l_u_e:

     A list with elements 

 def.box: default graphical parameters for 'maBoxplot'.

def.plot: default graphical parameters for 'maPlot'.

def.lines: default graphical parameters for functions such as
          'maLoessLines' used in 'maPlot'.

def.legend: default graphical parameters for functions such as
          'maLegendLines' used in 'maPlot'.

def.text: default graphical parameters for functions such as 'maText'
          used in 'maPlot'.

_A_u_t_h_o_r(_s):

     Sandrine Dudoit, <URL: http://www.stat.berkeley.edu/~sandrine>.

_R_e_f_e_r_e_n_c_e_s:

     S. Dudoit and Y. H. Yang. (2002). Bioconductor R packages for
     exploratory analysis and normalization of cDNA microarray data. In
     G. Parmigiani, E. S. Garrett, R. A. Irizarry and S. L. Zeger,
     editors, _The Analysis of Gene Expression Data: Methods and
     Software_, Springer, New York.

_S_e_e _A_l_s_o:

     'maBoxplot', 'maPlot', 'maLegendLines', 'maLoessLines', 'maText',
     'maDotsDefaults'.

_E_x_a_m_p_l_e_s:

     # See examples for maPlot.