plotFeatures           package:tilingArray           R Documentation

_P_l_o_t _g_e_n_o_m_i_c _f_e_a_t_u_r_e_s _f_o_r _a _r_e_g_i_o_n _a_l_o_n_g _a _c_h_r_o_m_o_s_o_m_e

_D_e_s_c_r_i_p_t_i_o_n:

     Plot genomic features for a region along a chromosome

_U_s_a_g_e:

     plotFeatures(gff, chr, xlim, strand, vpr, featureColorScheme=1, 
                  featureExclude=c("chromosome", "nucleotide_match", "insertion"),            
                  featureNoLabel=c("uORF", "CDS"), ...)

_A_r_g_u_m_e_n_t_s:

     gff: data frame with genome annotation from the GFF file.

     chr: integer of length 1 specifying the chromosome to plot the
          features for.

    xlim: integer of length 2 with start and end coordinates (in bases)
          for plotting.

  strand: character scalar which should be set to either '+' or '-' to 
          indicate which strand of DNA to plot the features from.

     vpr: which viewport to plot the features in.

featureColorScheme: numeric scalar, used to select a color scheme for
          the  boxes representing genomic features such as coding
          sequences, ncRNAs etc.  Currently the only value supported is
          1.

featureExclude: character vector of names of feature types (in gff)
          that should not be plotted. Default is '"chromosome"',
          '"nucleotide_match"' and  '"insertion"'.  Additional possible
          candidates include: '"ARS"', '"repeat_region"',
          '"repeat_family"' and '"nc_primary_transcript"'.

featureNoLabel: character vector, names of feature types (in gff) that
          should not be labelled with their names (if they are
          plotted).

     ...: additional arguments.

_D_e_t_a_i_l_s:

     This function is called by 'plotAlongChrom' when the 'gff'
     argument has been specified.  It should not be called directly by
     the user.

_A_u_t_h_o_r(_s):

     Wolfgang Huber <huber@ebi.ac.uk>

_E_x_a_m_p_l_e_s:

