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).
visGSEA(eTerm, which_sample = 1, which_term = "GO:0006281", weight = 1, orientation = c("vertical",
"horizontal"), newpage = T)
- an object of class "eTerm"
- which sample will be used. It can be index or
- which term will be used. It can be index or term ID
or term names
- type of score weigth. It can be "0" for unweighted (an
equivalent to Kolmogorov-Smirnov, only considering the rank), "1" for
weighted by input gene score (by default), and "2" for over-weighted,
and so on
- the orientation of the plots. It can be either
"vertical" (default) or "horizontal"
- logical to indicate whether to open a new page. By
default, it sets to true for opening a new page
#visGSEA(eTerm, which_sample=1, which_term=1)