plotSegmentationDots       package:tilingArray       R Documentation

_P_l_o_t _p_o_i_n_t_s _f_o_r _a _r_e_g_i_o_n _a_l_o_n_g _a _c_h_r_o_m_o_s_o_m_e

_D_e_s_c_r_i_p_t_i_o_n:

     Plot points for a region along a chromosome

_U_s_a_g_e:

     plotSegmentationDots(dat, xlim, ylim, ylab, threshold=NA, 
                          chr=1, strand="+", vpr, colors, main, 
                          pointSize=unit(0.6, "mm"), showConfidenceIntervals=TRUE, 
                          sepPlots=FALSE, cexAxisLabel=1, cexAxis=1,...)

_A_r_g_u_m_e_n_t_s:

     dat: list containing data to be plotted (see _Details_ section
          below for particulars).

    xlim: integer vector of length 2 with start and end coordinates (in
          bases) for plotting.

    ylim: numeric vector containing the y limits of the plot.

    ylab: character scalar (if 'sepPlots=FALSE') or vector containing
          y-axis label(s).

threshold: numeric scalar indicating the threshold of expression
          (default value is NA, for  no threshold.  If a value is
          supplied, it is subtracted from the intensity measures in
          'dat$y'.

     chr: integer of length 1 indicating the chromosome to be plot
          (defaults to 1).

  strand: character scalar which should be set to either '+' or '-' to 
          indicate which strand of DNA to plot the intensity values
          from (defaults to "+").

     vpr: which viewport to plot the figure in.  If this function is
          called directly  by the user this argument should be left
          missing.

  colors: named character vector, optional. If missing,  a default
          color scheme is used: 'c("+"="#00441b", "-"="#081d58",
          "duplicated"="grey", "cp"="#101010",  "highlight"="red",
          "threshold"="grey")',  where the first three elements refer
          to the colors of data points and the  last three to the
          colors of lines in the plot.

    main: character vector specifying plot title.

pointSize: an object of class unit which specifies the size of each
          point.  Default value is 'unit(0.6, "mm")'.

showConfidenceIntervals: logical scalar indicating whether confidence
          intervals for each change-point are to be plotted (only
          available once segmentation has occurred).

sepPlots: logical scalar indicating whether the intensities are plotted
          separately for each array (if 'dat$y' has multiple columns). 
          Defaults to FALSE, in which case the average intensity for
          each probe is plotted.  When TRUE, up to 3 arrays can be
          plotted separately (more than 3 gets crowded).

cexAxisLabel: numeric scalar specifying the magnification to be used
          for the y-axis label relative to the current test size.

 cexAxis: numeric scalar specifying the magnification to be used for
          the y-axis annotation relative to the current text size.

     ...: additional arguments.

_D_e_t_a_i_l_s:

     This function is called by 'plotAlongChrom' when the argument
     'what' is set to 'dots'.  Although this function can be called
     directly by the user, this is not recommended.

     The 'dat' list contains the following items: items 'x':
     x-coordinates (in bases) along chromosome, 

        1.  'y': intensity matrix of probes along chromosome,

        2.  'flag': indicates probe uniqueness in the genome. 
           Possibilities are 3: multiple perfect matches, 2: has no PM
           but one or more near-matches, 1: has exactly one PM and some
           near-matches in the genome, 0: has exactly one PM and no
           near-matches.

        3.  'extras': (optional) matrix of additional values (such as
           test-statistics/p-values) to be plotted.

_A_u_t_h_o_r(_s):

     Wolfgang Huber <huber@ebi.ac.uk>

_E_x_a_m_p_l_e_s:

