data(examplePosets)
plotPoset(examplePosets[["p1101"]])
## If you will be using that poset a lot, maybe simpler if
poset701 <- examplePosets[["p701"]]
plotPoset(poset701, addroot = TRUE)
## Compare to Pancreatic cancer figure in Gerstung et al., 2011
plotPoset(poset701,
names = c("KRAS", "SMAD4", "CDNK2A", "TP53",
"MLL3","PXDN", "TGFBR2"))
## If you want to show Root explicitly do
plotPoset(poset701, addroot = TRUE,
names = c("Root", "KRAS", "SMAD4", "CDNK2A", "TP53",
"MLL3","PXDN", "TGFBR2"))
## Of course, names are in the order of nodes, so KRAS is for node 1,
## etc, but the order of entries in the poset does not matter:
poset701b <- poset701[nrow(poset701):1, ]
plotPoset(poset701b,
names = c("KRAS", "SMAD4", "CDNK2A", "TP53",
"MLL3","PXDN", "TGFBR2"))
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