spatialDistribHits         package:RNAither         R Documentation

_P_l_o_t_t_i_n_g _t_h_e _s_p_a_t_i_a_l _d_i_s_t_r_i_b_u_t_i_o_n _o_f _t_h_e _h_i_t_s

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

     Plots the plates showing the spatial distribution of the hits
     using the ' plotPlate' function of the ' prada' package.

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

     spatialDistribHits(header, dataset, plotTitle, col4hits, col4anno, 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' 

plotTitle: the plot title 

col4hits: a character vector specifying the name of the dataset column
          containing the binary hit vector 

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

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:

     For each plate, the plot will be saved as a png file named after
     the experiment name specified in the header concatenated with the
     ' plotTitle', the number of the experiment, and the number of the
     plate.

     Wells containing positive controls are marked with a "P", wells
     containing negative controls with an "N".

     Each plate will also be saved as an html file containing
     mouse-overs with the siRNA name for each well.

     The function returns a list containing:

histoName : the plotname

c(minOfScreens, numOfScreens) : a vector with the number of the first
          experiment and of the last experiment

c(minOfPlates, numOfPlates) : a vector with the number of the first
          plate and the number of the last plate

_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", "Hits1", 0.05, 
     "GeneName", "pvalue_testfile1.txt")

     hitDataset1 <- scoredHits1[[1]]

     spatialDistribHits(header, hitDataset1, "Spatial distribution of hits", "Hits1", "GeneName", 1)

