imageplot               package:limma               R Documentation

_I_m_a_g_e _P_l_o_t _o_f _M_i_c_r_o_a_r_r_a_y _S_t_a_t_i_s_t_i_c_s

_D_e_s_c_r_i_p_t_i_o_n:

     Creates an image of shades of gray or colours, that represents the
     values of a statistic for each spot on the array. The statistic
     can be a log intensity ratio, quality information such as spot
     size or shape, or a t-statistic. This function can be used to
     explore whether there are any spatial effects in the data.

_U_s_a_g_e:

     imageplot(z, layout, low = NULL, high = NULL, ncolors = 123, zerocenter = NULL, 
     zlim = NULL, mar=rep(1,4), ...)

_A_r_g_u_m_e_n_t_s:

       z: numeric vector or array. This vector can contain any spot 
          statistics, such as log intensity ratios, spot sizes or
          shapes, or t-statistics. Missing values  are allowed and will
          result in blank spots on the image.

  layout: a list specifying the dimensions of the spot matrix and the
          grid matrix.

     low: color associated with low values of 'z'. May be specified as
          a character string  such as '"green"', '"white"' etc, or as a
          rgb vector in which 'c(1,0,0)' is red,  'c(0,1,0)' is green
          and 'c(0,0,1)' is blue. The default value is '"green"' if
          'zerocenter=T' or '"white"' if 'zerocenter=F'.

    high: color associated with high values of 'z'. The default value
          is '"red"' if 'zerocenter=T' or '"blue"' if 'zerocenter=F'.

 ncolors: number of color shades used in the image including low and
          high.

zerocenter: should zero values of 'z' correspond to a shade exactly
          halfway between the colors  low and high? The default is TRUE
          if 'z' takes positive and negative values,  otherwise FALSE.

    zlim: numerical vector of length 2 giving the extreme values of 'z'
          to associate with  colors 'low' and 'high'. By default 'zlim'
          is the range of 'z'. Any values of 'z' outside  the interval
          'zlim' will be truncated to the relevant limit.

     mar: numeric vector of length 4 specifying the width of the margin
          around the plot. This argument is passed to 'par'.

     ...: any other arguments will be passed to the function image

_D_e_t_a_i_l_s:

     The image follows the layout of an actual microarray slide with
     the bottom left corner representing the spot (1,1,1,1).  This
     function is very similar to the 'sma' function 'plot.spatial' but
     is intended  to display spatial patterns and artefacts rather than
     to highlight extreme  values. The function differs from
     'plot.spatial' most noticeably in that all the  spots are plotted
     and the image is plotted from bottom left rather than from  top
     left.

_V_a_l_u_e:

     An image is created on the current graphics device.

_A_u_t_h_o_r(_s):

     Gordon Smyth

_S_e_e _A_l_s_o:

     'maImage', 'image'.

     An overview of diagnostic functions available in LIMMA is given in
     6.Diagnostics.

_E_x_a_m_p_l_e_s:

     M <- rnorm(8*4*16*16)
     imageplot(M,layout=list(ngrid.r=8,ngrid.c=4,nspot.r=16,nspot.c=16))

