plot.cepa.all: plot the cepa.all object

In CePa: Centrality-Based Pathway Enrichment

plot the cepa.all object

Description

plot the cepa.all object

Usage

## S3 method for class 'cepa.all'
plot(x, id = NULL, cen = 1, type = c("graph", "null"), tool = c("igraph", "Rgraphviz"),
    node.name = NULL, node.type = NULL,
    adj.method = "none", only.sig = FALSE,
    cutoff = ifelse(adj.method == "none", 0.01, 0.05), ...)

Arguments

x	a cepa.all object
id	index or the name for the pathway
cen	index or the name for the centrality
type	If the aim is to plot single pathway, then this argument is to identify the kind of the plotting.
tool	Use which tool to visualize the graph. Choices are 'igraph' and 'Rgraphviz'
node.name	node.name for each node
node.type	node.type for each node
adj.method	method of p.adjust, available methods are "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none"
only.sig	whether to show all pathways. If just show significant pathways, the names for each significant pathway will be draw.
cutoff	cutoff for significance
...	other arguments

Details

This function has two applications. First, it can draw heatmaps of p-values of all pathways under different centrality measurements. To do it, users should set x, adj.method, only.sig, cutoff arguments.

Second, it can draw figures of single pathway under specific centrality measurement. Under this circumstance, this function is just a wrapper of plot.cepa. To do it, users should set x, id, cen, type, tool, node.name and node.type arguments. The id and cen arguments are used to get single cepa object that sent to the plot function.

It must be noted that these two kinds of arguments should not be mixed.

There is also another popular method qvalue to adjust p-values. However, errors may occur when adjusting some kind of p-value list by qvalue. So qvalue was not implemented into CePa. But still users can override the default p.adjust to support qvalue by themselves, see the vignette.

Author(s)

Zuguang Gu <[e-mail]>

See Also

cepa.all

Examples

## Not run: 
data(PID.db)

# ORA extension
data(gene.list)
# will spend about 20 min
res.ora = cepa.all(dif = gene.list$dif, bk = gene.list$bk, pc = PID.db$NCI)
plot(res.ora)
plot(res.ora, id = 3)
plot(res.ora, id = 3, 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.all(mat = eset, label = label, pc = PID.db$NCI)
plot(res.gsa)
plot(res.gsa, id = 3, cen = 2)
plot(res.gsa, id = 3, cen = 2, type = "null")

## End(Not run)

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