GOCluster {GOplot} | R Documentation |
Circular dendrogram.
Description
GOCluster generates a circular dendrogram of the data
clustering using by default euclidean distance and average linkage.The
inner ring displays the color coded logFC while the outside one encodes the
assigned terms to each gene.
Usage
GOCluster(data, process, metric, clust, clust.by, nlfc, lfc.col, lfc.min,
lfc.max, lfc.space, lfc.width, term.col, term.space, term.width)
Arguments
data |
A data frame which should be the result of
|
process |
A character vector of selected processes (ID or term description) |
metric |
A character vector specifying the distance measure to be used
(default='euclidean'), see |
clust |
A character vector specifying the agglomeration method to be
used (default='average'), see |
clust.by |
A character vector specifying if the clustering should be done for gene expression pattern or functional categories. By default the clustering is done based on the functional categories. |
nlfc |
If TRUE |
lfc.col |
Character vector to define the color scale for the logFC of the form c(high, midpoint,low) |
lfc.min |
Specifies the minimium value of the logFC scale (default = -3) |
lfc.max |
Specifies the maximum value of the logFC scale (default = 3) |
lfc.space |
The space between the leafs of the dendrogram and the ring for the logFC |
lfc.width |
The width of the logFC ring |
term.col |
A character vector specifying the colors of the term bands |
term.space |
The space between the logFC ring and the term ring |
term.width |
The width of the term ring |
Details
The inner ring can be split into smaller rings to display multiply logFC values resulting from various comparisons.
Examples
## Not run:
#Load the included dataset
data(EC)
#Generating the circ object
circ<-circular_dat(EC$david, EC$genelist)
#Creating the cluster plot
GOCluster(circ, EC$process)
#Cluster the data according to gene expression and assigning a different color scale for the logFC
GOCluster(circ,EC$process,clust.by='logFC',lfc.col=c('darkgoldenrod1','black','cyan1'))
## End(Not run)