prepareGenomePlot        package:quantsmooth        R Documentation

_S_e_t _u_p _a _f_u_l_l _g_e_n_o_m_e _p_l_o_t

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

     This function starts up a plot consisting of all chromosomes of a
     genomen, including axes with chromosome names.

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

     prepareGenomePlot(chrompos, cols = "grey50", paintCytobands = FALSE, bleach = 0, topspace = 1, organism, sexChromosomes = FALSE, ...)

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

chrompos: chrompos object, data.frame with 'CHR' column identifying 
          the chromosome of probes, and a 'MapInfo' column identifying 
          the position on the chromosome

    cols: color(s) for the chromosome lines

paintCytobands: logical, use 'paintCytoband' to plot ideograms for all
          chromosomes

  bleach: numeric [0,1], proportion by which to bleach the ideograms

topspace: numerical, extra space on top of plot, i.e. for legends

organism: character, if given a 2 column plot is created with the
          chromosomes  for the given species. Currently "hsa", "mmu",
          and "rno" are supported

sexChromosomes: logical, if 'TRUE' then also the sex chromosomes X and
          Y are plotted

     ...: extra arguments for 'plot' function

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

     If 'organism' is not supplied then a single column is plotted of
     the available  chromosomes in 'chrompos$CHR'. The arguments
     'paintCytobands', 'bleach', and 'sexChromosomes' are not used in
     that case.

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

     A matrix with 2 columns that contain the Y and X positions for the
     probes on the plot

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

     Jan Oosting

