identifyLines          package:geneplotter          R Documentation

(_D_e_p_r_e_c_a_t_e_d) _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:

     (This function is deprecated, and will be removed from a
     subsequent release) 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:

        ## Not run: 
        ## This function is deprecated, and not exported from the name space
        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")
       ## End(Not run)

