chipAlongChrom             package:Ringo             R Documentation

_V_i_s_u_a_l_i_z_e _C_h_I_P _i_n_t_e_n_s_i_t_i_e_s _a_l_o_n_g _t_h_e _c_h_r_o_m_o_s_o_m_e

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

     This function can visualize the array intensities from a ChIP chip
     experiment for a chromosomal region or the whole chromosome. It's
     loosely based on the 'plotAlongChrom' function from the package
     'tilingArray', but provides a different visualization.

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

     chipAlongChrom(eSet, chrom, probeAnno, xlim, ylim = NULL, 
      samples = NULL, paletteName = "Dark2", colPal = NULL,
      byStrand = FALSE, ylabel = "Intensity", rugCol = "#000010",
      itype = "p", ipch ="-", icex = 3, ilwd = 2, ilty = 1, useGFF = TRUE,
      gff = NULL, featCol = "darkblue", zero.line = TRUE, putLegend = TRUE,
      add = FALSE, verbose = TRUE, ...)

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

    eSet: An expression set containing the (normalized) ChIP
          intensitites. Can be generated by using the function
          'asExprSet'.

   chrom: character; the chromosome to visualizate

probeAnno: Environment holding genomic position, index and gene
          association of probes on array. See 'scripts/makeProbeAnno.R'
          for how to generate such an environment.

    xlim: start and end genomic coordinates on the chromosome to
          visualize

    ylim: minimum and maximum probe intensities for the plot, if
          'NULL'(defaul) set as 'range(exprs(eSet))'

 samples: numerc; which samples from the 'eSet' are to be shown.
          Default is to show all samples in the 'eSet',

paletteName: character; Name of the RColorBrewer palette to use for
          sample colors. If the number of samples is above the paletter
          size, random colors are taken.

  colPal: vector of colors to use for the sample intensities. This is
          alternative to the argument 'paletteName' for specifying
          which colors to use.

byStrand: logical; not implemented yet.

  ylabel: character; label for the y-axis, passed on to the plotting
          function as 'ylab'

  rugCol: color to use for marking the probe positions on the x-axis
          (genomic coordinate) 

   itype: character; type of plot type to use for the sample
          intensities. Defaults to "p".

    ipch: plot character to use with 'itype="p"'

    icex: character expansion to use for plotting symbol

    ilwd: line width of plotted lines if 'itype="l"'

    ilty: line type of plotted lines if 'itype="l"'; passed on to
          'par(lty)'.

  useGFF: use further annotation

     gff: Data frame containing annotation for genomic feature to be
          used to further annotate the plot.

 featCol: color to use for genomic features.

zero.line: logical; should a dashed horizontal line at y=0 be put into
          the plot?

putLegend: logical; should a legend be put into the plot?

     add: logical; should expression set intensities be plotted onto
          current device instead of a new one?

 verbose: logical; progress output to STDOUT.

     ...: further parameters passed on to 'plot.default', see details

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

     the following 'plot.default' arguments are already defined by
     arguments of this function and thus may not be included in '...':
     'xlim, ylim, col, pch, cex, lwd, lty, frame.plot'

_V_a_l_u_e:

     returns 'invisible' matrix of probe intensities in the selected
     genomic regions

_N_o_t_e:

     Use the function 'alongChrom' for alternative ways to display
     probe intensities in genomic regions.

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

     Joern Toedling toedling@ebi.ac.uk

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

     'alongChrom'

_E_x_a_m_p_l_e_s:

       ringoExampleDir <- system.file("exData",package="Ringo")
       load(file.path(ringoExampleDir,"exampleProbeAnno.rda"))
       load(file.path(ringoExampleDir,"exampleX.rda"))
       chipAlongChrom(exampleX, chrom="8", xlim=c(60208500,60216000),
                      ylim=c(-1,6), colPal=2:3, probeAnno=exProbeAnno,
                      gff=exGFF)  

