plotSegmentedGenome         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:

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

_A_r_g_u_m_e_n_t_s:

     ...: Objects of class '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

  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

  colors: vector of colors to plot segmented states of each 'SegList'
          passed to the function.

mark.regions: Boolean.  If true will colour code the segmentation plot
          using the information stored in $regions and generated by
          nudSegmentation, or an equivalent method.

    main: Specify the title of the plot

_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):

     Mike Smith

_S_e_e _A_l_s_o:

     'genomePlot' 'SegList'

_E_x_a_m_p_l_e_s:

