chipAlongChrom             package:Ringo             R Documentation

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_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 = "fold change [log]", rugCol = "#000010",
      itype = "r", ipch = 20, icex = 1, ilwd = 3, ilty = 1, useGFF = TRUE,
      gff = NULL, featCol = "darkblue", zero.line = TRUE, putLegend = TRUE,
      add = FALSE, maxInterDistance = 200,  coord=NULL, verbose = TRUE, ...)

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

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

   chrom: character; the chromosome to visualize

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'(default) set as 'range(exprs(eSet))'

 samples: numeric; 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 greater than the
          palette 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. Can be "r","u", or any of the 'type'
          specifications used in 'plot.default'. Defaults to "r".
          Please refer to the details section below.

    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?

maxInterDistance: numeric; only used when 'itype' is either "r" or "u";
          specifies the maximal distance up to which adjacent probe
          positions should be connected by a line.

   coord: optional integer of length 2; can be used instead of 'xlim'
          to specify the start and end coordinates of the genomic
          region to plot

 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'

     The 'itype' argument specifies the desired type of plot. It can be
     any valid specification of the 'type' argument in 'plot.default'
     or one of two special types:

     "_r" *r*estricted drawing of position-connecting lines. adjacent
          probe connections will be connected by a line only if less or
          equal to argument 'maxInterDistance' apart from each other;
          each probe position will be marked by an individual point
          anyway (whose shape is determined by the argument 'ipch').

     "_u" similar as "r" but the lines and the points will be
          *u*nconnected; reminiscent of 'plot.default''s 'type' "b".

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

     '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:

     'plot.default'; 'plotAlongChrom' in package 'tilingArray'

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

       # load data
       ringoExampleDir <- system.file("exData",package="Ringo")
       load(file.path(ringoExampleDir,"exampleProbeAnno.rda"))
       load(file.path(ringoExampleDir,"exampleX.rda"))

       # show a gene that is well represented on this microarray
       chipAlongChrom(exampleX, chrom="9", xlim=c(34318000,34321000),
                      ylim=c(-2,4), probeAnno=exProbeAnno, gff=exGFF)

