plotSegmentationHeatmap     package:tilingArray     R Documentation

_P_l_o_t _a _h_e_a_t_m_a_p _d_i_a_g_r_a_m _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 a heatmap diagram for a region along a chromosome

_U_s_a_g_e:

     plotSegmentationHeatmap(dat, xlim, ylab, rowNames, 
                             chr=1, strand="+", vpr, colors,                 
                             colHeatmap=colorRamp(brewer.pal(9, "YlGnBu")), 
                             showConfidenceIntervals=TRUE,
                             just=c("left","centre"),
                             main, ...)

_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.

    ylab: character scalar specifying y-axis label.

rowNames: character vector specifying a name for each row in the
          heatmap plot.

     chr: integer of length 1 indicating the chromosome to 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 colors of data points and the  last three to those of
          lines in the plot.

colHeatmap: function describing color scheme for the heatmap plot
          (defaults to 'YlGnBu' from RColorBrewer package).

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

    just: character vector specifying the justification of the supplied
          values to the given coordinates; setting the first entry to
          "left" indicates that the supplied x-coordinates are the
          start positions of the probes, change this to "centre" if the
          x-coordinates are the probe middle positions. Usually the
          second entry should be "centre" (see 'grid.rect')

    main: character vector specifying plot title.

     ...: additional arguments.

_D_e_t_a_i_l_s:

     This function is called by 'plotAlongChrom' if the argument 'what'
     is set to 'heatmap'. Although this function can be called directly
     by the user, this is not recommended. The 'dat' list contains the
     following items:

     '_x' x-coordinates (in bases) along chromosome

     '_y' intensity matrix of probes along chromosome

     '_f_l_a_g' 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.

     '_e_x_t_r_a_s' (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>

