visGSEA: Function to visualise running enrichment score for a given...

In dnet: Integrative Analysis of Omics Data in Terms of Network, Evolution and Ontology

Description

visGSEA is supposed to visualise running enrichment score for a given sample and a gene set. To help understand the underlying running enrichment score, the input gene scores are also displayed. Positions for members in the given gene set are color-coded in both displays (red line for the positive gene scores, and green line for the negative).

Usage

visGSEA(
eTerm,
which_sample = 1,
which_term = "GO:0006281",
plot = T,
orientation = c("vertical", "horizontal"),
hit.linewidth = 0.5,
newpage = T
)

Arguments

eTerm	an object of class "eTerm"
which_sample	which sample will be used. It can be index or sample names
which_term	which term will be used. It can be index or term ID or term names
plot	logical to indicate whether to plot
orientation	the orientation of the plots. It can be either "vertical" (default) or "horizontal"
hit.linewidth	the line width for the hits (ie genes in the gene set)
newpage	logical to indicate whether to open a new page. By default, it sets to true for opening a new page

Value

leading genes (being sorted)

Note

none

See Also

dGSEA, dGSEAview

Examples

#visGSEA(eTerm, which_sample=1, which_term=1)

dnet documentation built on Feb. 20, 2020, 5:08 p.m.