parallel.coordinates {rflowcyt} | R Documentation

## Parallel coordinates: Plotting each observation across all variables

### Description

To view multi-dimensional data, a parallel coordinates plot is made such that each row is treated as an observation which is plotted across all column variables. The two dimensional plot which results has the column variables on the horizontal axis and the values of the column variables on the vertical axis. Care should be taken to note that each line drawn corresponds to a row observation. Also the units of measurements should be the same among all column variables. Note that the row observations can be grouped visually by specifying group line options such as line type, color, or width. The data can also be scaled to have a range of (0,1).

### Usage

      parallel.coordinates(x, varlabpos=1:dim(x)[2],
                           variable.names=colnames(x),my.ylab ="",
                           my.ylim =c(min(x),max(x)),
                           at.y=seq(min(x), max(x),
                                by=(max(x)-min(x))/20),
                           each.ylab=at.y, scaled = FALSE,
                           group = rep(1, dim(x)[1]),
                           group.lty=group, group.col=group,
                           group.lwd=group, superimpose=FALSE)

### Arguments

`x` | matrix of the data (rows are the observations & columns are the variables)
`varlabpos` | numerical vector denoting the position of the variables/variable labels on the horizontal axis; default is a vector of 1 to the number of variables
`variable.names` | a vector of strings denoting the names of each variable; default value is the column names of the input matrix, x
`my.ylab` | character string denoting the name/label of the vertical y-axis; default value is "Values"
`my.ylim` | two-dimensional vector denoting the range of the vertical y-axis, ie, the range of the variables; default is the vector of the min and the max of the input matrix, x
`at.y` | vector of the vertical y-axis values at which labels will be shown on the plot; default is a vector of the minimum to the maximum by increments of one-twentieth of the difference between the mininum and the maximum
`each.ylab` | vector of the vertical y-axis labels; default is the numerical values of at.y
`scaled` | boolean; if TRUE, then the data is scaled to a range of [0,1]
`group` | a vector of indicating which group the row observations are in; default is all the row observations are in one group
`group.lty` | vector corresponding to each data row's line type corresponding to the group that each row observation is in; default is the vector value of group
`group.col` | vector corresponding to each data row's line type corresponding to the group that each row observation is in; default is the vector value of group
`group.lwd` | vector corresponding to each data row's line type corresponding to the group that each row observation is in; default is the vector value of group
`superimpose` | Boolean, if TRUE then parallel coordinate lines will be added to the existing plot; otherwise a new parallel coordinate plot will be made; default is FALSE

### Value

A parallel coordinates plot in which row observations are plotted across all column variables in a plot with x-axis= names of the column variables and y-axis=values of the column variables.

### WARNING

The dataset may have to be subsetted before implementing this function because the plot may take a long time to finish and may not be readable.

If the at.y option is not within the range of the column variables, then the range will be changed appropriately, but the interval or the difference between two elements of at.y will remain the same in order to keep the specified spacings of the y labels/tick marks.

If the each.ylab vector is different in length with the number of tick marks specified by at.y for the vertical axis, then by default the each.ylab will be the values of at.y. In other words, the labels will be the number values specified by at.y.

### Author(s)

A.J. Rossini, J.Y. Wan

### See Also

`pairs`, `plot`, `ImageParCoord`

### Examples

    if (require(rfcdmin)){
      data.there<-is.element("MC.053",objects())
        if ((sum(data.there) != length(data.there))) {
          ## obtaining the FCS objects from FHCRC data
          data(MC.053min)
        }

      dataMC<-MC.053@data

      if (interactive()) {
       par(mfrow=c(2,2))

        ### subset the data to the first 5 observations because it is too huge
        parallel.coordinates(dataMC[c(1:5),-6])
        ### the first 2 rows are a group and the last 3 rows are a different group
        parallel.coordinates(dataMC[c(1:5),-6], group=c(1,1,2,2,2))

        ### the same plot is scaled to 0,1 range
        parallel.coordinates(dataMC[c(1:5),-6], scaled=TRUE)
        parallel.coordinates(dataMC[c(1:5),-6], scaled=TRUE, group=c(1,1,2,2,2))

        parallel.coordinates(dataMC[c(1:5),1:4])
        ## changing the positions of the variables to the 1st, 5th, 8th, 16th
        ## positions on the horizontal x-axis
        parallel.coordinates(dataMC[c(1:5),1:4], varlabpos=c(1, 5, 8, 16))

        parallel.coordinates(dataMC[c(1:5),1:3])
        ## having the variable positions out of order of how they are plotted
        parallel.coordinates(dataMC[c(1:5),1:3], varlabpos=c(1, 15, 8))

        ## changing the labels of the vertical y-axis
        parallel.coordinates(dataMC[c(1:5),1:3], at.y=c(0, 500,
        1000),my.ylim=c(0, 1000),
        each.ylab=c("zero", "five hundred", "one thou"))
      }
    }

[Package rflowcyt version 1.0.1 Index]