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, hc = TRUE, boxplot = TRUE, hist = TRUE, returnTree=FALSE)
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 (array samples) on the dendrogram will be coloured by class. |
hc |
Logical. Draw dendrogram of hierarchical cluster analysis of cases. Default is TRUE |
boxplot |
Logical. Draw boxplot. Default is TRUE |
hist |
Logical. Draw histogram. Default is TRUE |
returnTree |
Logical. Return the hieracrhical cluster analysis results. Default is FALSE |
... |
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$train) print(class(logkhan)) overview(logkhan, title="Subset of Khan Training data") overview(logkhan, classvec=khan$train.classes, labels=khan$train.classes)