pairs.CSP {rflowcyt} | R Documentation

## Contour/Hexbin Scatterplot Matrices

### Description

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

### Usage

    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)"))

### Arguments

`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)"

### Details

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.

### Value

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.

### Author(s)

J.Y. Wan and A.J. Rossini

### References

Hexbin, other papers.

### See Also

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

### Examples

      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)
        }
      }

[Package rflowcyt version 1.4.0 Index]