cPlot              package:geneplotter              R Documentation

_A _p_l_o_t_t_i_n_g _f_u_n_c_t_i_o_n _f_o_r _c_h_r_o_m_o_s_o_m_e_s.

_D_e_s_c_r_i_p_t_i_o_n:

     Given a chromLocation object, will plot all the gene locations
     from that object.

_U_s_a_g_e:

     cPlot(plotChroms, useChroms=chromNames(plotChroms),
           scale=c("relative","max"), fg="white", bg="lightgrey", 
           glen=0.4, xlab="", ylab="Chromosome",  main = organism(plotChroms))

_A_r_g_u_m_e_n_t_s:

plotChroms: An object of type chromLocation which contains all the gene
          information to be plotted. 

useChroms: A vector of chromosome names to be used in the plot. Default
          is to use all the chromosomes from the plotChroms object.

   scale: Passed on to cScale as it's scale argument.  Determines
          whether the graph is scaled on a relative or absolute basis.

      fg: The colour to be used for the genes.  Default is white.

      bg: The colour to be used for the background of the plot.
          Defaults to lightgrey/

    glen: A scaling factor applied to the plotted length of each gene. 
          Defaults to 0.4 - it is recommended that this not be set
          larger then 0.5 as it will cause overlap between chromosomes.

    xlab: A label for the x axis.

    ylab: A label for the y axis.

    main: A main label for the plot.

_D_e_t_a_i_l_s:

     This function will first use the lengths of the chromosomes,
     stored in the object to create scaling factors for the X axis. 
     Once the scaling factors are determined, the 'chromLocation'
     object which is passed in is used to determine all the gene
     locations/strand information/etc, which is then plotted for the
     user.

_A_u_t_h_o_r(_s):

     Jeff Gentry

_S_e_e _A_l_s_o:

     'cScale', 'cColor', 'chromLocation-class'

_E_x_a_m_p_l_e_s:

        ## 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), add=TRUE)
        if (require(hgu95av2)) {
         z <- buildChromLocation("hgu95av2")

          if (interactive()) {
            par(ask=TRUE)
          }

          for (sc in c("max","relative"))
            cPlot(z,c("1","5","10","X","Y"),sc)
       } else print("This example can not be run without hgu95av2 data package")

