dotplotArrays          package:BeadExplorer          R Documentation

_P_l_o_t_s _a _s_e_r_i_e_s _o_f _d_o_t_p_l_o_t_s _f_o_r _B_e_a_d_C_h_i_p _Q_C _d_a_t_a

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

     Plots a series of dotplots for BeadChip QC data

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

     dotplotArrays(beadData, beadQC, qc, col = NULL, currentcol = "black", meansym = 4, arraysym = 19, currentsym = 19, 
     meansize = 1.5, arraysize = 1.5, currentsize = 1.5,  savegraph = "png", extension = "_Arrays", width = 1200, height = 800, 
     legend = TRUE, verbose = TRUE, ...)

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

beadData: Object of class 'beadData-class' 

  beadQC: Object of class 'beadQC-class' 

      qc: 'data.frame' generated by 'link{readQC}' 

     col: A vector of colours used for each array type 

currentcol: Colour to use for the current array 

 meansym: Symbol to use for the mean 

arraysym: Symbol to use to represent each array 

currentsym: Symbol to use to represent the current array 

meansize: Size to use for the mean symbol

arraysize: Size to use for the array symbol

currentsize: Size to use for the current symbol

savegraph: Character to specify the output type ("png","bmp" or "jpeg") 

extension: Character to add to the output file name  

   width: Width in pixels of graph output 

  height: Height in pixels of graph output

  legend: Logical, indicating if a legend should be added 

 verbose: Logical, indicating if commentray should be used 

     ...: arguments passed to 'dotplotQC' 

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

     A graph of a dotplot of QC measures is produced.  The function
     compares QC values for the current beadData and beadQC objects to
     QC values from previous run analyses that have been stored in the
     log file (qc).  The function is similar to 'boxplotArrays' except
     that the data is plotted as a dot plot rather than a box plot. 
     This function is the choice where the number of previous analyses
     in the log file is small.

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

     None

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

     Gareth Elvidge gareth.elvidge@well.ox.ac.uk

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

     'boxplotArrays', 'help'

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

     ## Not run: 
     data(examplebeadData)
     data(examplebeadQC)
     data(exampleQC)
     dotplotArrays(examplebeadData, examplebeadQC, exampleQC)
     ## End(Not run)

