scatterPlot           package:BeadExplorer           R Documentation

_P_a_i_r_w_i_s_e _s_c_a_t_t_e_r_g_r_a_p_h _o_f _d_a_t_a

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

     Plots a scattergraph of intensity data for two samples

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

     scatterPlot(beadData, xcol, ycol, manifest=NULL, equalline=TRUE, equallinecol="red", equallinetype=1, identify=TRUE, lines=2, 
     linescol="green", linestype=2, log=TRUE, xlab="", ylab="", highlight=TRUE, detection=0.99, 
     highlightcol=c("red","blue","green"), legend=TRUE, ...)

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

beadData: Object of class 'beadData-class'

    xcol: Numeric, column number to plot on x-axis 

    ycol: Numeric, column number to plot on y-axis

manifest: 'data.frame' of manifest data - produced by 'readManifest'

equalline: Logcial, specifiying if an equality line should be plotted
          on the graph

equallinecol: Colour to be used for the equality line 

equallinetype: Line type used for an equality line, see 'par' -lty 

identify: Logcial, specifiying if an interactive point and click plot
          identification tool should be used 

   lines: Numeric, a vector of fold change lines to plot 

linescol: Colour to be used for the fold change lines 

linestype: Line type to be used for the fold change lines , see
          'par'-lty

     log: Logcial, specifying if log2 axes should be used 

    xlab: A label for the x-axis 

    ylab: A label for the y-axis 

highlight: Logcial, specifying whether to highlight the points by
          detection score 

detection: The illumina cut-off detection score called as 'Present' 

highlightcol: A vector of colours to be used for present calls 

  legend: Logical, specifying if a legend should be drawn 

     ...: Arguments passed to 'plot' 

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

     This function produces a scattergraph of two samples.  Use
     identify to allow the clicking of data points with a  left-click
     of the mouse.  Finish selecting data points by right-clicking the
     mouse and 'stop'. Data (eg log2 intensity, ratio, detection
     scores) of the selected points is outputted to the console.  Using
     the manifest argument will also output gene annotation information
     of selected points.

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

     If identify is used, information regarding the points selected by
     the mouse is returned

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

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

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

     pairs

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

     data(examplebeadData)
     scatterPlot(examplebeadData, 1,2)

     #to include annotation data:-
     #man<-readManifest("d:\Bead_Set_Manifest\Human_WG-6.csv")
     #scatterPlot(examplebeadData, 1, 2, man)

