plotCopa                package:copa                R Documentation

_P_l_o_t _G_e_n_e _P_a_i_r_s _f_o_m _t_h_e _R_e_s_u_l_t_s _o_f _R_u_n_n_i_n_g _c_o_p_a

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

     This function can be used to visualize pairs of genes that may be
     involved in recurrent gene fusion in cancer.

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

     plotCopa(copa, idx, lib = NULL,  sort = TRUE, col = NULL, legend = 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.

    sort: Boolean. Should the data be sorted before plotting? Defaults
          to 'TRUE'.

     col: A vector of color names or numbers to be used for coloring
          the different samples in the resulting barplot.

  legend: A vector of terms describing the two sample types (e.g.,
          'Normal' and 'Tumor'). Defaults to 'NULL'

_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)
     plotCopa(tmp, 1, col = c("red", "blue"))
     }

