pairs.CSP              package:rflowcyt              R Documentation

_C_o_n_t_o_u_r/_H_e_x_b_i_n _S_c_a_t_t_e_r_p_l_o_t _M_a_t_r_i_c_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     A pairs plotting of histograms and rectangular-binned or
     hexagonal-binned image plots are produced using 'hist' and
     'ContourScatterPlot', respectively.

_U_s_a_g_e:

     pairs.CSP(x,
               status=NULL,
               box.idx.list=NULL,
               type.CSP=c("count.diff",
                       "p.hat",
                       "p.hat.norm",
                       "z.stat"),
               alternate.hexbinplot=FALSE,
               n.hexbins=100,
               range.x=range(x),
               varlabpos=round(seq(range.x[1],
                     ceiling(diff(range.x)/150)*150+range.x[1],
                     by=150),0),
               cutoffs = seq(range.x[1],
                       ceiling(diff(range.x)/25)*25+range.x[1],
                       by=25),  

                labels = colnames(x),

                panel = ContourScatterPlot,
                main="",
                         
                image.col=heat.colors(10),
                numlev=5,...,
                lower.panel = legend.CSP,
                upper.panel = panel,
                overlay.panel=rect.box.idx,
                border.boxes=1:length(box.idx.list),
                lwd.boxes=rep(3,length(box.idx.list)),
                lty.boxes=rep(1,length(box.idx.list)),
                           
                label.pos = 0.5 + has.diag/3,
                cex.labels = NULL,
                font.labels = 1,
                row1attop = TRUE,
                gap=1,
                ch.col=c("heat.colors(n)",
                        "rainbow(n, start=.7, end=.1)",
                        "terrain.colors(n)",
                        "topo.colors(n)",
                        "cm.colors(n)"))

_A_r_g_u_m_e_n_t_s:

       x: matrix of data in which the columns are the variables and the
          rows are the individual observations

  status: numerical binary 0, 1 vector denoting the status of the
          observations; default is NULL

box.idx.list: a list of vectors indicating the positions of 'x' which
          form a box to be overlayed on the binned plot in the upper
          and lower panels of the hexbin plot and the only the upper
          panel of the rectangular-binned plot by default 

type.CSP: character string denoting the type of value to be estimated
          using the 'status' for each cell grid: the difference in
          counts ("count.diff"), the proportion ("p.hat"), the
          normalized proportion at 0.5 ("p.hat.norm"), the z.statistic
          ("z.stat"), see make.density for details.

alternate.hexbinplot: Boolean; if TRUE then alternate hexbin pairs plot
          is used; otherwise the ContourScatterPlot with rectangular
          bins is implemented

n.hexbins: number of bins for hexbin call; default is 100

 range.x: vector denoting the min and the max of the observation values
          across all variable columns

varlabpos: vector of position of the variable values in which to label
          the x and y axes 

 cutoffs: the cutoffs for the x and y axes of the rectangular bins when
          alternate.hexbinplot is FALSE

  labels: the labels for the diagonals when alternative.hexbinplot is
          TRUE

   panel: default panel function; currently this is the contour scatter
          plot with rectangular bins; this option is ignored when
          'alternate.hexbinplot' is TRUE

    main: the main title for the rectanglar Contour scatter plot when
          alternative.hexbinplot is FALSE

image.col: image colors for the rectangular bins when
          alternative.hexbinplot is FALSE

  numlev: number of levels for the contours for the rectangular bins
          when alternative.hexbinplot is FALSE

     ...: other options in 'hexagons' or 'ContourScatterPlot'

lower.panel: function for the lower panels of the pairs plot; currently
          this is fixed as a hexbin (when 'alternate.hexbinplot' is
          TRUE) or the legend.CSP (when 'alternative.hexbinplot' is
          FALSE) 

upper.panel: function for the upper panels of the pairs plot; currently
          this is fixed as a hexbin or contour scatter plot  

overlay.panel: Function which describes the overlay image on the
          panels; currently this option only works with the
          'rect.box.idx' function and other functions that have the
          same signature

border.boxes: vector of corresponding border colors for each of the
          boxes in 'box.idx.list'

lwd.boxes: vector of corresponding widths for each of the outlined
          boxes in 'box.idx.list'; default is for all the boxes to have
          lwd = 3

lty.boxes: vector of corresponding line types for each of the outlined
          boxes in 'box.idx.list'; default is for all the boxes to have
          lty = 1

label.pos: position of the labels on the diagonal panels which are
          currently fixed as histograms; this option is not in use
          currently.

cex.labels: cex for the labels, used only when 'alternative.hexbinplot'
          is TRUE 

font.labels: font for the labels, used only when
          'alternative.hexbinplot' is TRUE 

row1attop: boolean if row 1 is at the top, used only when
          'alternative.hexbinplot' is TRUE 

     gap: used only when 'alternative.hexbinplot' is TRUE  

  ch.col: character string denoting the type of color palette used for
          the rectangular-binned image to be displayed in the legend
          when 'aternate.hexbinplot' is FALSE; default is
          "heat.colors(n)"

_D_e_t_a_i_l_s:

     There are no legends for the hexagonal (when
     'alternate.hexbinplot' is TRUE) but there is a roughly estimate
     legend available for the rectangular binning (when
     'alternate.hexbinplot' is FALSE) in the pairs plot.

_V_a_l_u_e:

     A pairs plot is displayed.  NOTE: The histograms on the diagonals
     are of the whole dataset regardless of the value of the cells in
     each ContourScatterPlot.

_A_u_t_h_o_r(_s):

     J.Y. Wan and A.J. Rossini

_R_e_f_e_r_e_n_c_e_s:

     Hexbin, other papers.

_S_e_e _A_l_s_o:

     objects to See Also as 'hexbin' in the 'hexbin' package

_E_x_a_m_p_l_e_s:

       if (interactive()){
         if (require(rfcdmin)){
           data.there<-is.element(c("st.1829", "unst.1829", "st.DRT",
                         "unst.DRT"),objects())

           if ( ( sum(data.there) != length(data.there) )){
              ## obtaining the FCS objects from VRC data
             data(VRCmin)
           }

           ## subsetting the data for quicker plot display of less data
           data.mat1<-st.DRT@data[1:10000, 1:5]

           ## hexagonal binning

           pairs.CSP(data.mat1, alternate.hexbinplot=TRUE)

           ## rectangular binning with legends 

           pairs.CSP(data.mat1, numlev=3,
              image.col=heat.colors(20))

           ## rectangular binning without legends 

           pairs.CSP(data.mat1, numlev=3,
              image.col=heat.colors(20),
              lower.panel=ContourScatterPlot)

           ## putting a box around the observations
           ## greater than 500 for the second variable
           ##  less than 200 for the first variable
           idx1<-which(data.mat1[,2] > 500)  ## green box
           idx2<-which(data.mat1[,1] < 200)  ## blue box

           box.idx.list<-list(idx1, idx2)
           ## hexbin plots
           pairs.CSP(data.mat1, box.idx.list=box.idx.list,
                 alternate.hexbinplot=TRUE, border.vec=c("green", "blue"))
           ## rectangular binned plots
           pairs.CSP(data.mat1, box.idx.list=box.idx.list,
                 alternate.hexbinplot=FALSE,border.vec=c("green", "blue"),
                 lower.panel=ContourScatterPlot)
         }
       }

