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

Description Usage Arguments Details Author(s) See Also Examples

View source: R/plot_print.R

Description

plot the cepa.all object

Usage

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## 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 <z.gu@dkfz.de>

See Also

cepa.all

Examples

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## 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 March 26, 2020, 6:24 p.m.