cColor              package:geneplotter              R Documentation

_A _f_u_n_c_t_i_o_n _f_o_r _m_a_r_k_i_n_g _s_p_e_c_i_f_i_c _p_r_o_b_e_s _o_n _a _c_P_l_o_t.

_D_e_s_c_r_i_p_t_i_o_n:

     Given a set of probes, will highlight them in the color desired on
     a plot which has already been created via the function cPlot().

_U_s_a_g_e:

     cColor(probes, color, plotChroms, scale=c("relative","max"),glen=0.4)

_A_r_g_u_m_e_n_t_s:

  probes: The probes that are being highlighted.

   color: The color to highlight the probes.

plotChroms: An object of type 'chromLocation' which contains all the
          gene information to be plotted. 

   scale: Whether to plot the graph scaled absolutely or relative by
          chromosome.  Default is absolute.

    glen: The length of the gene line plotted

_D_e_t_a_i_l_s:

     It is important to call the function 'cPlot()' first.  This
     function will then search for the specific locations of the probes
     desired, which are contained within the 'plotChroms' instance of a
     'chromLocation' class.  It will then pass these on to the plotting
     routine to highlight the desired locations.  NOTE:  It is
     important that 'plotChroms', 'scale' and 'glen' parameters are the
     same as used for 'cPlot()'.

_A_u_t_h_o_r(_s):

     Jeff Gentry

_S_e_e _A_l_s_o:

     'cPlot', 'chromLocation-class'

_E_x_a_m_p_l_e_s:

        ## A bit of a hack to not have a package dependency on hgu95av2
        ## but need to fiddle w/ the warn level to not fail the example anyways.
        curWarn <- options(warn=0)
        on.exit(options(warn=curWarn), add=TRUE)
        if (require(hgu95av2)) {

          z <- buildChromLocation("hgu95av2")
          cPlot(z)
          probes <- c("266_s_at", "31411_at", "610_at", "failExample")
          cColor(probes, "red", z)
          probes2 <- c("960_g_at", "41807_at", "931_at", "39032_at")
          cColor(probes2, "blue", z)
      } else print("Need hgu95av2 data package to run example")

