makeRectangleOverlay      package:GenomeGraphs      R Documentation

_C_r_e_a_t_e _a _r_e_c_t_a_n_g_u_l_a_r _o_v_e_r_l_a_y

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

     Construct ractangular overlays.

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

     makeRectangleOverlay(start, end, region = NULL, coords = c("genomic", "absolute"), dp = NULL)

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

   start: Start position in coords coordinates 

     end: End position in coords coordinates 

  region: Which tracks to span, or the y (vertical range) 

  coords: Which coordinate system to use, if absolute then the range is
          from 0,1 and region become the y coordinates 

      dp: The display parameters 

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

     The rectangular overlay can be used to plot overlays in either
     genomic or absolute coordinates. If coordinates are absolute then
     the region argument becomes the y arguments.

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

     An object of class RectangleOverlay

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

     data("exampleData", package = "GenomeGraphs")
     cop <- makeGenericArray(intensity  = cn, probeStart = probestart, 
                             dp = DisplayPars(size=3, color = "seagreen", type="dot"))
     gdPlot(list(makeGenomeAxis(), cop), overlays =
            makeRectangleOverlay(start = 180350000, end = 180350000 + 1e5, dp = DisplayPars(alpha = .3)))

