plotAlongChromLegend       package:tilingArray       R Documentation

_P_l_o_t _a _l_e_g_e_n_d _f_o_r _g_e_n_o_m_i_c _f_e_a_t_u_r_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     Plot a legend for genomic features

_U_s_a_g_e:

     plotAlongChromLegend(vpr, nr=2, 
         featureColorScheme=1, 
         featureExclude=c("chromosome", "nucleotide_match", "insertion"),
         mainLegend, cexLegend=0.35, cexMain=1)

_A_r_g_u_m_e_n_t_s:

     vpr: vector specifying where to place the legend in figure (set up
          by using the  'viewport' function from the grid package. 
          When this function is called directly  by the user this
          argument should be left missing.

      nr: numeric scalar, specifying the number of rows to plot legend
          over  (default value is 2).

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"'.

mainLegend: character vector specifying legend title.

cexLegend: numeric scalar specifying the magnification to be used for
          the legend  text relative to the current text size.

 cexMain: numeric scalar specifying the magnification to be used for
          the legend  title relative to the current text size.

_D_e_t_a_i_l_s:

     This function is usually called by 'plotAlongChrom' when
     'doLegend' is TRUE.  It can also be called directly by the user to
     produce a separate legend.  

     The following features are included in the legend (unless excluded
     using the 'featuredExclude' option): '"chromosome"',
     '"nucleotide_match"', '"pseudogene"', '"uORF"',
     '"nc_primary_transcript"', '"region"', '"repeat_family"',
     '"repeat_region"', '"transposable_element"',
     '"transposable_element_gene"', '"ARS"', '"centromere"',
     '"telomere"', '"insertion"', '"CDS"', '"CDS_dubious"', '"ncRNA"',
     '"tRNA"', '"snRNA"', '"rRNA"', '"snoRNA"', '"binding_site"' and
     '"TF_binding_site"'.

_A_u_t_h_o_r(_s):

     Wolfgang Huber <huber@ebi.ac.uk>

_E_x_a_m_p_l_e_s:

     ## plotAlongChromLegend(mainLegend="Legend")

