overview {made4} | R Documentation |
Very simple wrapper function that draws a boxplot, histogram and hierarchical tree of expression data
overview(dataset, labels=NULL, title="", classvec=NULL, ...)
dataset |
a matrix , data.frame ,
exprSet or marrayRaw .
If the input is gene expression data in a matrix or data.frame . The
rows and columns are expected to contain the variables (genes) and cases (array samples)
respectively. |
labels |
Vector, labels to be placed on samples in plots. Default is rownames(dataset) |
title |
Character, label to be placed on plots. Default is NULL |
classvec |
A factor or vector which describes the classes in columns of the
dataset . Default is NULL. If included columns will be coloured by class. |
... |
further arguments passed to or from other methods |
The hierarchical plot is produced using average linkage cluster analysis with Eisen's correlation metric.
Aedin Culhane
See also as boxplot
, hclust
,
hist
data(khan) logkhan<-log2(khan$train) overview(logkhan, title="Subset of Khan Training data") overview(logkhan, classvec=khan$train.classes, labels=khan$train.classes)