volcanoPlot             package:RNAither             R Documentation

_M_a_k_i_n_g _a _v_o_l_c_a_n_o _p_l_o_t

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

     Makes a volcano plot of the data.

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

     volcanoPlot(header, dataset, col4plotx, col4ploty, col4anno, plotTitle, sigLevel, showPlot)

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

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

 dataset: an R data frame generated with 'generateDatasetFile' 

col4plotx: a character vector specifying the name of the column
          containing the intensity values, usually ' SigIntensity' 

col4ploty: a character vector specifying the name of the dataset column
          containing the corresponding p-values 

col4anno: a character string specifying the name of the dataset column
          to be used to define the replicate, e.g. ' "GeneName"' or '
          "Internal_GeneID"'. 

plotTitle: the plot title 

sigLevel: the significance level for the p-value, indicating where a
          horizontal green line will be drawn 

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:

     Plots the intensity values against the negative decadic logarithm
     of the p-values. A green horizontal line is drawn at the specified
     significance level.

     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'

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

     data(exampleHeader, package="RNAither")
     data(pValVec1, package="RNAither")
     data(scoredDataset1, package="RNAither")

     ##for details on the generation of pValVec1 and scoredDataset1, see the example of the Ttest function linked above.

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

     hitDataset1 <- scoredHits1[[1]]
     hitvector1 <- scoredHits1[[2]]

     volcano_name <- volcanoPlot(header, hitDataset1, "SigIntensity", "pValue.ttest_l", "GeneName", 
     "Volcano Plot", 0.05, 1)

