xGSEAdotplotR Documentation

Function to visualise GSEA results using dot plot

Description

xGSEAdotplot is supposed to visualise GSEA results using dot plot. It returns an object of class "ggplot" or a list of "ggplot" objects.

Usage

xGSEAdotplot(eGSEA, top = 1, priority.color = c("lightyellow",
"orange"),
peak = TRUE, compact = FALSE, signature = TRUE)

Arguments

eGSEA

an object of class "eGSEA"

top

the number of the top enrichments to be visualised. Alternatively, the gene set names can be queried

priority.color

a character vector for coloring priority scores

peak

logical to indicate whether the peak info of leading genes is labelled

compact

logical to indicate whether the compact/void theme is used. If TRUE, axes and legend info will be hidden

signature

logical to indicate whether the signature is assigned to the plot caption. By default, it sets TRUE showing which function is used to draw this graph

Value

an object of class "ggplot" or a list of "ggplot" objects.

Note

none

See Also

xPierGSEA

Examples

## Not run: 
# Load the library
library(Pi)

## End(Not run)
RData.location <- "http://galahad.well.ox.ac.uk/bigdata_dev"
## Not run: 
gp <- xGSEAdotplot(eGSEA, top=1)
#gp <- xGSEAdotplot(eGSEA, top=1, peak=FALSE, compact=TRUE, signature=FALSE)
gp

ls_gp <- xGSEAdotplot(eGSEA, top=1:4, signature=FALSE)
library(gridExtra)
grid.arrange(grobs=ls_gp, ncol=2)

## End(Not run)