maImage.func             package:marray             R Documentation

_C_o_l_o_r _i_m_a_g_e _f_o_r _c_D_N_A _m_i_c_r_o_a_r_r_a_y _s_p_o_t _s_t_a_t_i_s_t_i_c_s

_D_e_s_c_r_i_p_t_i_o_n:

     This function creates spatial images of shades of gray or colors
     that correspond to the values of a statistic for each spot on the
     array. The statistic can be the intensity log-ratio M, a spot
     quality measure (e.g. spot size or shape), or a test statistic.
     This function can be used to explore whether there are any spatial
     effects in the data, for example, print-tip or cover-slip effects.
     This function is called by 'maImage'.

_U_s_a_g_e:

     maImage.func(x, L, subset=TRUE, col=heat.colors(12), contours=FALSE, overlay=NULL, ol.col=1,  ...)

_A_r_g_u_m_e_n_t_s:

       x: A "numeric" vector of spot statistics.

       L: An object of class '"marrayLayout"', if L is missing we will
          assume the dimension of x.

  subset: A "logical" or "numeric" vector indicating the subset of
          spots to display on the image.

     col: A list of colors such as that generated by rainbow,
          heat.colors, topo.colors, terrain.colors, or similar
          functions. In addition to these color palette functions, a
          new function  'maPalette' was defined to generate color
          palettes from user supplied low, middle, and high color
          values.

contours: If 'contours=TRUE', contours are plotted, otherwise they are
          not shown.

 overlay: A logical vector of spots to be highlighted on the image
          plots.

  ol.col: Color of the overlay spots.

     ...: Optional graphical parameters, see 'par'.

_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:

     'image', 'maImage', 'maColorBar', 'maPalette'.

_E_x_a_m_p_l_e_s:

     # See examples for image.