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 colors or shades of gray that represent the
     values of a statistic for each spot on a spotted microarray. This
     function can be used to explore any spatial effects across the
     microarray.

_U_s_a_g_e:

     imageplot(z, layout, low = NULL, high = NULL, ncolors = 123, zerocenter = NULL, 
     zlim = NULL, mar=c(2,1,1,1), legend=TRUE, ...)

_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. Infinite values are not
          allowed.

  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'.

  legend: logical, if 'TRUE' the range of 'z' and 'zlim' is shown in
          the bottom margin

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

_D_e_t_a_i_l_s:

     This function may be used to plot the values of any spot-specific
     statistic, such as the log intensity ratio, background intensity
     or a quality measure such as spot size or shape. The image follows
     the layout of an actual microarray slide with the bottom left
     corner representing the spot (1,1,1,1). The color range is used to
     represent the range of values for the statistic. When this
     function is used to plot the red/green log-ratios, it is intended
     to be an in silico version of the classic false-colored
     red-yellow-green image of a scanned two-color microarray.

     This function is related to the earlier 'plot.spatial' function in
     the 'sma' package and to the later 'maImage' function in the
     'marray' package. It 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. It is intended to display
     spatial patterns and artefacts rather than to highlight only the
     extreme values as does 'plot.spatial'. It differs from 'maImage'
     in that any statistic may be plotted and in its use of a
     red-yellow-green color scheme for log-ratios, similar to the
     classic false-colored jpeg image, rather than the red-black-green
     color scheme associated with heat maps.

_V_a_l_u_e:

     An plot 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
     09.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))

