HighlightRegion-class      package:GenomeGraphs      R Documentation

_C_l_a_s_s "_H_i_g_h_l_i_g_h_t_R_e_g_i_o_n" _i_s _u_s_e_d _t_o _h_i_g_h_l_i_g_h_t _v_e_r_t_i_c_a_l _b_l_o_c_k_s _o_f
_g_e_n_o_m_i_c _r_e_g_i_o_n_s.

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

     HighlightRegion is used to highlight a genomic region of interest.
     The class offers the ability to highlight or block out regions of
     interest.

_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("HighlightRegion", ...)'.

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


     '_s_t_a_r_t': Object of class '"numeric"' genomic start position. 

     '_e_n_d': Object of class '"numeric"' genomic end position. 

     '_r_e_g_i_o_n': Object of class '"numericOrNull"' start and end number
          of the tracks to be covered by the region. These start from
          the first track (top = 1) to the last track:
          'length(gdObjects)' in the call to 'gdObject'

     '_c_o_o_r_d_s': Object of class '"character"' can be either "genomic" or
          "absolute", if the coordinates are "absolute" then one can
          plot things using the coordinate space defined by: lower-left
          (0,0) upper-right (1,1). In this case, start = x0, end = x1
          and then region = (y0, y1). See the examples for more
          details. 

     '_d_p': Object of class '"DisplayPars"' specifys the various display
          parameters.


_E_x_t_e_n_d_s:

     Class '"gdObject"', directly.

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

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

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

     James Bullard

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

     if (interactive()) {
     data("exampleData", package="GenomeGraphs")

     ga <- new("GenomeAxis")
     grF <- new("GeneRegion", start = 10000, end = 20000, chromosome = "I", strand = "+", biomart = yeastMart)
     grR <- new("GeneRegion", start = 10000, end = 20000, chromosome = "I", strand = "-", biomart = yeastMart)
     bt <- new("BaseTrack", base = yeastCons1[,1], value = yeastCons1[,2])
     hr1 <- new("HighlightRegion", start = 11000, end = 13000,
                dp = DisplayPars(alpha = 1, color = "red", lty = "dashed", lwd = 3))
     hr2 <- new("HighlightRegion", start = 15900, end = 16500)
               
     gdPlot(list(grF, ga, grR, bt), highlightRegions = list(hr1, hr2))
     }

