scatterPlotCopa             package:copa             R Documentation

_C_r_e_a_t_e _s_c_a_t_t_e_r_p_l_o_t_s _o_f _i_n_t_e_r_e_s_t_i_n_g _g_e_n_e _p_a_i_r_s

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

     This function allows one to create scatterplots of gene pairs that
     may be involved in recurrent gene fusion in cancer.

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

     scatterPlotCopa(copa, idx, lib = NULL)

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

    copa: An object of class 'copa', resulting from a call to the
          'copa' function

     idx: A numeric vector listing the gene pairs to plot (e.g., idx =
          1:3 will plot the first three gene pairs).

     lib: If the underlying data are Affymetrix expression values, one
          can specify an annotation package and the plot labels will be
          extracted from the xxxSYMBOL environment. If 'NULL', the
          'row.names' of the gene expression matrix will be used.

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

     Note that this function will output all the gene pairs in the idx
     vector without pausing. This can be controlled by either setting
     par(ask = TRUE), or by redirecting the output to a file (using
     e.g., 'pdf', 'ps', etc.).

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

     This function is called solely for outputting plots. No values are
     returned.

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

     James W. MacDonald

_R_e_f_e_r_e_n_c_e_s:

     Tomlins, SA, et al. Recurrent fusion of TMPRSS2 and ETS
     transcription factor genes in prostate cancer. Science. 2005 Oct
     28;310(5748):644-8.

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

     if(interactive()){
     library(Biobase)
     data(sample.ExpressionSet)
     cl <- abs(3 - as.numeric(pData(sample.ExpressionSet)[,2]))
     tmp <- copa(sample.ExpressionSet, cl)
     scatterPlotCopa(tmp, 1)
     }

