plot.cepa: Plot the cepa object

In CePa: Centrality-Based Pathway Enrichment

Plot the cepa object

Description

Plot the cepa object

Usage

## S3 method for class 'cepa'
plot(x, type = c("graph", "null"), ...)

Arguments

x	a cepa object
type	identify the type for the plot
...	arguments passed to plotGraph

Details

The function is wrapper of plotGraph and plotNull. If type is specified to "graph", the graph of the network will be plotted (see plotGraph for details). If type is specified to "null", the null distribution of the pathway score in the pathway will be plotted (see plotNull for details).

Value

if type is set to "graph", the function will return a igraph object or a graphML object of the pathway. Else it is NULL.

Author(s)

Zuguang Gu <[e-mail]>

See Also

cepa, plotNull, plotGraph

Examples

## Not run: 

data(PID.db)

# ORA extension
data(gene.list)
# will spend about 20 min
res.ora = cepa(dif = gene.list$dif, bk = gene.list$bk, pc = PID.db$NCI, id = 2)
plot(res.ora)
plot(res.ora, type = "null")

# GSA extension
# P53_symbol.gct and P53_cls can be downloaded from
# http://mcube.nju.edu.cn/jwang/lab/soft/cepa/
eset = read.gct("P53_symbol.gct")
label = read.cls("P53.cls", treatment="MUT", control="WT")
# will spend about 45 min
res.gsa = cepa(mat = eset, label = label, pc = PID.db$NCI, id = 2)
plot(res.gsa, type = "null")

## End(Not run)

CePa documentation built on Oct. 8, 2024, 5:08 p.m.