seekGSEplot: GSEA plot
In Solatar/seeqR:

Description Usage Arguments Value Examples

Imports: ggplot2, fgsea, AnnotationDbi, GO.db, org.Hs.eg.db, org.Mm.eg.db

seekGSEplot(
  rankedList,
  setID,
  setList = "BP",
  Species = NA,
  gseaTable = NA,
  annotations = c("up", "down"),
  plotTitle = NA,
  cutC = log2(1.5),
  gseaParam = 1,
  vlines = T,
  hlines = T,
  lineSize = 1.5,
  ticksSize = 0.2,
  textSize = 30,
  annoSize = 10,
  colors = c("red", "blue", "green"),
  yTitle = T,
  xTitle = T,
  xText = T,
  ggarrangeRows = 1
)

`rankedList`	A vector sorted from high to low values of the ranking metric (e.g. log2 fold change), with names according to entrezids.
`setID`	string, either GO-ID (e.g. "GO:0006355") or name of a custom set included in the setList
`setList`	either string ("BP", "CC" or "MF") or a list of custom datasets, where each item in the list is a vector of strings (entrezids)
`Species`	a string, either "human" or "mouse". Is used to retreive the right Entrez IDs for the GO pathways. Unimportant if a custom setID is used.
`gseaTable`	data.frame, direct output from seekGSEA. Adds statistics to the plot.
`annotations`	vector of 2 strings, which will be written underneath the color ribbon
`plotTitle`	string, replaces the gene set name as the plot title
`cutC`	log2FC threshold, changes the vlines and the color ribbon
`gseaParam`	GSEA parameter determines ES-gain per hit (default: 1)
`vlines`	boolean, vertical lines indicate the log2FC threshold
`hlines`	boolean, horizontal lines indicate the ES scores
`lineSize`	width of main line through the plot
`textSize`	text size for plot title, axis titles and axis labels
`annoSize`	text size for annoations (below color ribbon) and statistics
`colors`	vector with 3 strings, naming the colors used for: upregulated ribbon, downregulated ribbon, main line
`yTitle`	boolean, should there be a title for the y axis?
`xTitle`	boolean, should there be a title for the x axis?
`xText`	boolean, should there be a x axis labels?
`tickSize`	width of ticks in the barcode (default: 0.2)

ggplot object

myDE <- sqDE
rl <- seekGSErl(myDE[[1]])
mygsea <- seekGSEA(rl, Species="mouse", setList="BP")
seekGSEplot(rl, setID="GO:0006355", Species="mouse", gseaTable=mygsea)