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]