genomePlot              package:snapCGH              R Documentation

_P_l_o_t_s _t_h_e _g_e_n_o_m_e

_D_e_s_c_r_i_p_t_i_o_n:

     Basic plot of the log2 ratios for each array ordered along the
     genome.

_U_s_a_g_e:

     genomePlot(input, array = 1, naut = 22, Y = FALSE, X
                      = FALSE, main = NA, status, values, pch, cex, col, chrominfo =
                      chrominfo.Mb, ylim = c(-2, 2), ylb = "Log2Ratio",
                      chrom.to.plot = NA, xlim = c(0,NA), ...)

_A_r_g_u_m_e_n_t_s:

   input: an object of class 'MAList' or 'SegList'

   array: integer of the array (sample) to be plotted.

    naut: number of autosomes in the organism

       Y: TRUE if chromosome Y is to be plotted, FALSE otherwise

       X: TRUE if chromosome X is to be plotted, FALSE otherwise

    main: Provides the title of the plot

  status: character vector giving the control status of each spot on
          the array, of same length as the number of rows of
          'log2ratios(input)'. If omitted, all points are plotted in
          the default color, symbol and size.

  values: character vector giving values of 'status' to be highlighted
          on the plot. Defaults to unique values of 'status'. Ignored
          if there is no 'status' vector.

     pch: vector or list of plotting characters. Default to integer
          code 16. Ignored is there is no 'status' vector.

     col: numeric or character vector of colors, of the same length as
          'values'. Defaults to '1:length(values)'. Ignored if there is
          no 'status' vector.

     cex: numeric vector of plot symbol expansions, of the the same
          length as 'values'. Defaults to 0.2 for the most common
          'status' value and 1 for the others. Ignored if there is no
          'status' vector.

chrominfo: a chromosomal information associated with the mapping of the
          data.

    ylim: Minimum y-scale to use for plotting.

chrom.to.plot: Specify which chromosome to plot

     ylb: label for the Y-axis.

    xlim: limits for the x-axis

     ...: Any other parameters

_D_e_t_a_i_l_s:

     The status vector is intended to specify the control status of
     each spot, for example "gene", "ratio control", "house keeping
     gene", "buffer" and so on. The vector is usually computed using
     the function controlStatus and a spot-types file. However the
     function may be used to highlight any subset of spots.

_A_u_t_h_o_r(_s):

     John Marioni

_S_e_e _A_l_s_o:

     'MAList' 'SegList'

