vennDiag              package:RNAither              R Documentation

_P_l_o_t_t_i_n_g _a _V_e_n_n _D_i_a_g_r_a_m _t_o _c_o_m_p_a_r_e _h_i_t_s

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

     Plots a Venn Diagram of up to three binary hit vectors.

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

     vennDiag(header, listOfCols, listOfNames, plotTitle, showPlot)

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

  header: the header of a dataset file generated with
          'generateDatasetFile' 

listOfCols: a list of binary hit vectors to compare 

listOfNames: a list of character strings for the annotation of the Venn
          Diagram 

plotTitle: the plot title 

showPlot: 0 or 1. 1 will open one or several plot windows in the R GUI,
          0 will only save the plot(s) without opening windows 

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

     The plot is saved in a pdf and a png file named after the
     experiment name specified in the header concatenated with the '
     plotTitle'.

     The function returns the plot name.

_S_e_e _A_l_s_o:

     'Ttest', 'MannWhitney'

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

     data(exampleHeader, package="RNAither")

     data(pValVec1, package="RNAither")
     data(pValVec2, package="RNAither")
     data(scoredDataset1, package="RNAither")
     data(scoredDataset2, package="RNAither")

     ##for details on the generation of pValVec and scoredDataset, 
     ##see the examples of the functions Ttest and MannWhitney linked above.

     scoredHits1 <- hitselectionPval(scoredDataset1, pValVec1, "SigIntensity", "pValue.ttest_l", 0.05, 
     "GeneName", "pvalue_testfile1.txt")

     scoredHits2 <- hitselectionPval(scoredDataset2, pValVec2, "SigIntensity", "pValue.mannwhitney_l", 0.05, 
     "GeneName", "pvalue_testfile2.txt")

     hitvector1 <- scoredHits1[[2]]
     hitvector2 <- scoredHits2[[2]]

     plot_name <- vennDiag(header, list(hitvector1, hitvector2), list("t test", "Mann-Whitney test"), 
     "Venn diagram", 1)

