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

Examples

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

Source code

visGSEA.r

Source man

visGSEA.Rd visGSEA.pdf

See also

dGSEA, dGSEAview