GenomeAxis-class        package:GenomeGraphs        R Documentation

_C_l_a_s_s "_G_e_n_o_m_e_A_x_i_s", _r_e_p_r_e_s_e_n_t_i_n_g _a _g_e_n_o_m_i_c _c_o_o_r_d_i_n_a_t_e _a_x_i_s

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

     Represents a genomic coordinate axis

_O_b_j_e_c_t_s _f_r_o_m _t_h_e _C_l_a_s_s:

     Objects can be created by calls of the form 'new("GenomeAxis",
     ...)'.

_S_l_o_t_s:


     '_a_d_d_5_3': Object of class '"logical"', indicating if 5 to 3 prime
          direction needs to be plotted

     '_a_d_d_3_5': Object of class '"logical"', indicating if 3 to 5 prime
          direction needs to be plotted 

     '_d_p': Object of class '"DisplayPars"', containing the display
          parameters such as size of the plot and color

     '_l_i_t_t_l_e_T_i_c_k_s': Object of class '"logical"', indicating if the
          genome axis should be dense for improved locating of regions
          of interest.

_M_e_t_h_o_d_s:

     No methods defined with class "GenomeAxis" in the signature.

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

     Steffen Durinck

_R_e_f_e_r_e_n_c_e_s:

     http://www.stat.berkeley.edu/~steffen/

_S_e_e _A_l_s_o:

     objects to See Also as 'gdPlot'

_E_x_a_m_p_l_e_s:

     if(interactive()){
     mart = useMart("ensembl", dataset="hsapiens_gene_ensembl")
     genomeAxis = new("GenomeAxis", add53=TRUE)
     plusStrand = new("GeneRegion", chromosome = "17", start = 30450000, end = 30550000, strand = "+", biomart = mart)
     gdPlot(list(genomeAxis, plusStrand), minBase = 30450000, maxBase =  30550000)
     }

