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),...)
x |
a list of fluorescent data from one (or more) FCS object(s) |
varpos |
the numerical column variable position of the data of the FCS object |
... |
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.fluors) ## 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.fluors[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.fluors[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) } ##Extract fluorescent information from the serie of FCS files drug.fluors<-lapply(drugData,fluors) ##Draw a boxplot for the Foward SCatter parameter ##for the differents aliquots (of the same cell line) ##tested with different compounds. boxplot.FCS(drug.fluors,varpos=c(1),col=c(1:8),main="FSC of differents aliquots from the same cell line treated with different compounds.")