plot.cepa: Plot the cepa object
In jokergoo/CePa: Centrality-Based Pathway Enrichment

Description Usage Arguments Details Value Author(s) See Also Examples

Plot the cepa object

1 2	## S3 method for class 'cepa' plot(x, type = c("graph", "null"), ...)

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

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).

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

Zuguang Gu <z.gu@dkfz.de>

cepa, plotNull, plotGraph

## 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
# https://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)