identifyLines          package:geneplotter          R Documentation

_A _f_u_n_c_t_i_o_n _f_o_r _i_d_e_n_t_i_f_y_i_n_g _s_a_m_p_l_e _l_i_n_e_s _o_n _a_n _a_l_o_n_g_C_h_r_o_m()
_p_l_o_t.

_D_e_s_c_r_i_p_t_i_o_n:

     Given an environment returned from alongChrom(), will call
     identify() on the alongChrom() plot.

_U_s_a_g_e:

     identifyLines(identEnvir,...)

_A_r_g_u_m_e_n_t_s:

identEnvir: An environment created by alongChrom.

     ...: Any extra arguments are passed on to identify().

_D_e_t_a_i_l_s:

     The environment contains two vectors of points - "X" and "Y" are
     their labels, and contain the X and Y points respectively.  These
     vectors are extracted out of the environment and fed into an
     identify() call (with some extra processing to get the labeling
     correct.)  As with identify(), one need only to right click to
     exit from the function.

_A_u_t_h_o_r(_s):

     Jeff Gentry

_S_e_e _A_l_s_o:

     'alongChrom', 'identify'.

_E_x_a_m_p_l_e_s:

        data(sample.exprSet)

        ## 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")
          lty <- c(1, 2, 3, 4, 5)
          cols <- c("red", "green", "blue", "orange", "magenta", "black")
          identEnv <- alongChrom(sample.exprSet,"1", z, xloc="equispaced",
                               plotFormat="cumulative", scale="none",
                               lty,cols)
          if (interactive()) {
            identifyLines(identEnv)
          }
       } else print("This example needs the hgu95av2 data package")