boxplot.FCS {rflowcyt} | R Documentation

## Create boxplots one parameter of one (or more) FCS object(s)

### Description

Produce box-and-whisker plot(s) of a single column variable specified from the data of one (or more) FCS object(s).

### Usage

    boxplot.FCS(x, varpos=c(1),groups=NULL, xlab, ylab, col,
    alternating=TRUE, do.out = FALSE, ...)

### Arguments

`x` | a list of one (or more) FCS object(s) or a cytoSet object
`varpos` | the numerical column variable position of the data of the FCS object
`groups` | a variable or expression to be evaluated in the data frame specified by 'data', expected to act as a grouping variable within each panel, typically used to distinguish different groups by varying graphical parameters like color and line type
`xlab` | a title for the x axis
`ylab` | a title for the y axis
`col` | The colors for lines and points. Multiple colors can be specified so that each point can be given its own color. If there are fewer colors than points they are recycled in the standard fashion. Lines will all be plotted in the first colour specified.
`alternating` | logical specifying whether axis labels should alternate from one side of the group of panels to the other (for more details see `xyplot`)
`do.out` | logical to specify if the outlier values should be displayed (default is FALSE)
`...` | any other arguments are passed to the `boxplot` function

### Details

If several FCS objects are supplied parallel boxplots will be plotted. Other options from the functions `plot`, `boxplot`.

### Value

The `boxplot` will output a list with the following components:

`stats` | a matrix, each column contains the extreme of the lower whisker, the lower hinge, the median, the upper hinge and the extreme of the upper whisker for one group/plot.
`n` | a vector with the number of observations in each group
`conf` | a matrix where each column contains the lower and upper extremes of the notch
`out` | the values of any data points which lie beyond the extremes of the whiskers
`group` | a vector of the same length as out whose elements indicate which group the outlier belongs to
`names` | a vector of names for the groups

### Author(s)

N. Le Meur

### See Also

`boxplot`, `boxplot.stats`

### Examples

     ## Example I:
     require(rfcdmin)
     data(flowcyt.data)

     ## Draw a boxplot for the Foward Scatter parameter for the time points 1
     ## and 6 (in this experiment, each time point corresponds to a column of
     ## a 96 wells plates)
     mat <- matrix(c(1:2),1,2,byrow=TRUE)
     nf <- layout(mat,respect=TRUE)
     boxplot.FCS(flowcyt.data[1:8],varpos=c(1),col=c(1:8),main="FSC across stains time point 1",names=paste("stain",c(1:8),sep=""))
     boxplot.FCS(flowcyt.data[65:72],varpos=c(1),col=c(1:8),main="FSC across stains time point 9",names=paste("stain",c(1:8),sep=""))

     ##Example II:
     ## Read a serie of FCS files
     if (require(rfcdmin)) {

     ##obtaining the location of the fcs files in the data
      pathFiles<-system.file("bccrc", package="rfcdmin")
      drugFiles<-dir(pathFiles)

     ## reading in the FCS files
      drugData<-read.series.FCS(drugFiles,path=pathFiles,MY.DEBUG=FALSE)
      }

     ##Draw a boxplot for the Foward Scatter parameter
     ##for the differents aliquots (of the same cell line)
     ##tested with different compounds.
     boxplot.FCS(drugData,varpos=c(1),col=c(1:8),main="FSC of differents aliquots from the same cell line treated with different compounds.")

[Package rflowcyt version 1.16.0 Index]