plotNull: Plot the null distribution of the pathway score

In CePa: Centrality-Based Pathway Enrichment

Plot the null distribution of the pathway score

Description

Plot the null distribution of the pathway score

Usage

plotNull(x)

Arguments

x	a cepa object

Details

There are two figures in the plotting.

• A) Distribution of node score in the pathway under simulation. Since a pathway contains a list of nodes. The distribution of node score for the pathway in each simulation is measures by maximum value, the 75th quantile, median value and minimum value. The distribution of node score for the pathway in the real data is highlighted.

• B) Histogram of simulated pathway scores.

The function is always called through plot.cepa.all and plot.cepa.

Author(s)

Zuguang Gu <[e-mail]>

See Also

cepa, plot.cepa

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)
ora = get.cepa(res.ora, id = 5, cen = 3)
plotNull(ora)

# 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)
gsa = get.cepa(res.gsa, id = 5, cen = 3)
plotNull(gsa)

## End(Not run)

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