alongChrom            package:geneplotter            R Documentation

_A _f_u_n_c_t_i_o_n _f_o_r _p_l_o_t_t_i_n_g _e_x_p_r_e_s_s_i_o_n _d_a_t_a _f_r_o_m _a_n _e_x_p_r_s_e_t _f_o_r _a
_g_i_v_e_n _c_h_r_o_m_o_s_o_m_e.

_D_e_s_c_r_i_p_t_i_o_n:

     Given a particular exprset object, a chromLocation object, and a
     chromosome name, will plot selected exprSet data using various
     methods.

_U_s_a_g_e:

        alongChrom(eSet, chrom, specChrom,  xlim, whichGenes, 
        plotFormat=c("cumulative", "local","image"),
        xloc=c("equispaced", "physical"), 
        scale=c("none","zscale","rankscale","rangescale","zrobustscale"),
        geneSymbols=FALSE, byStrand=FALSE, colors="red", lty=1, type="S",
        ...)

_A_r_g_u_m_e_n_t_s:

    eSet: The exprset object to be used.

   chrom: The desired chromosome.

specChrom: An object of type chromLocation for the species being
          represented.

    xlim: A pair of values - either character or integer, which will
          denote the range of genes to display (based on base pair:
          either directly in the case of integers, or using the
          locations of the named genes if character).  If not supplied,
          the entire chromosome is used.

whichGenes: If supplied, will limit the displayed genes to the ones
          provided in this vector.

    xloc: Determines whether the X axis points (gene names) will be
          displayed according to their relative position on the
          chromosome (physical), or spaced evenly (equispaced). 
          Default is equispaced.

plotFormat: Determines the method which to plot the data.

   scale: Determines what method of scaling will be applied to the
          data.  Default is none.

geneSymbols: Notes whether to use Affy IDs or Gene Symbols, default is
          Affy IDs

byStrand: Determines whether to show the entire plot at once, or a
          split plot by strands.  Default is a singular plot

     lty: A vector of line types, which will be cycled. 

    type: Plot type, from par.  Defaults to "S".

  colors: A vector of colors for the plots, which will be cycled.

     ...: Any remaining graphics commands may be passed along as per
          plot()

_D_e_t_a_i_l_s:

     The genes on the chromosome of interest are extracted from the
     'chromLocation' object passed in, which are then intersected with
     the genes listed in the exprset.  These remaining genes will then
     be plotted according to the 'plotFormat' argument.  If 'image' is
     specified, an image plot is created showing the expression levels
     of the samples by gene, using a colour map to denote the levels. 
     If 'cumulative' is chosen, the cumulative expression level is
     plotted against the genes for each sample.  Likewise, if 'local'
     is used, the raw data is plotted for each sample against the genes
     using a boxplot format.

     Not all parameters are honored for all plotformats.  'xloc',
     'lty', and 'type' are only used with the 'cumulative' plotformat.

_A_u_t_h_o_r(_s):

     Jeff Gentry

_E_x_a_m_p_l_e_s:

        data(sample.exprSet)
        ## A bit of a hack to not have a package dependency on hgu95av2
        ## but need to fiddle w/ the warn level to not fail the example anyways.
        curWarn <- options(warn=0)
        on.exit(options(warn=curWarn$warn), add=TRUE)
        if (require(hgu95av2)) {
           z <- buildChromLocation("hgu95av2")
           lty <- c(1, 2, 3, 4, 5)
           cols <- c("red", "green", "blue", "orange", "magenta", "black")
           cols <- cols[sample.exprSet$cov3]
           if (interactive()) {
              par(ask=TRUE)
           }

           ## Here we're using xlim to denote a physical region to display
           xlim <- c(87511280,127717880)
           for (xl in c("equispaced", "physical"))
             for (sc in c("none","rangescale"))
             {
                alongChrom(sample.exprSet, "1", z, xlim=xlim, xloc=xl,
                   plotFormat="cumulative", scale=sc,lty=lty, col=cols)
             }

          ## Here we're looking for specific genes
          which <- c("31540_at","31583_at", "31508_at", "31529_at", "31439_f_at",
                    "31729_at")
          ## Gene "31529_at" does not exist in the current set of genes,
          ## here it demonstrates how genes not available are dropped.
           for (xl in c("equispaced", "physical"))
             for (sc in c("none","rangescale"))
             {
                 alongChrom(sample.exprSet, "1", z, which=which, xloc=xl,
                    plotFormat="cumulative", scale=sc,lty=lty, col=cols)
              }

           ## Do an image plot
           for (bs in c(TRUE,FALSE))
              alongChrom(sample.exprSet, "1",z, xlim=xlim, plotFormat="image",
                        scale="zscale", byStrand=bs)

           ## A boxplot
           for (st in c(TRUE,FALSE))
              alongChrom(sample.exprSet, "1", z, plotFormat="local",
                         colors=cols, byStrand=st)
         } else print("Example can not be run without the hgu95av2 data package")