boxplot.FCS {rflowcyt} | R Documentation |
Produce box-and-whisker plot(s) of a single column variable specified from the data of one (or more) FCS object(s).
boxplot.FCS(x, varpos=c(1),groups=NULL, xlab, ylab, col, alternating=TRUE, do.out = FALSE, ...)
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 |
If several FCS objects are supplied parallel boxplots will be
plotted.
Other options from the functions plot
,
boxplot
.
The boxplot
will output a list with the following components:
stats |
|
n |
|
conf |
|
out |
|
group |
|
names |
a vector of names for the groups
N. Le Meur
## 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.")