GOplot (version 1.0.2)

GOCluster: 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 circle_dat in case the data contains only one logFC column. Otherwise data is a data frame whereas the first column contains the genes, the second the term and the following columns the logFCs of the different contrasts.

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 dist

clust

A character vector specifying the agglomeration method to be used (default='average'), see hclust

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 data contains multiple logFC columns (default= FALSE)

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)