OncoSimulR (version 2.2.2)

plot.fitnessEffects: Plot fitnessEffects objects.

Description

Plot the restriction table/graph of restrictions, the epistasis, and the order effects in a fitnessEffects object.

Usage

"plot"(x, type = "graphNEL", layout = NULL,
expandModules = FALSE, autofit = FALSE,
scale_char = ifelse(type == "graphNEL", 1/10, 5),
return_g = FALSE, lwdf = 1, ...)

Arguments

x

A fitnessEffects object, as produced by allFitnessEffects.

type

Whether you want a "graphNEL" or an "igraph" graph.

layout

For "igraph", the layout. For example, if you know you really have only a tree you might want to use layout.reingold.tilford. Note that there is very limited support for passing options, etc. In most cases, it is either the default or the layout.reingold.tilford.

expandModules

If there are modules with multiple genes, if you set this to TRUE modules will be replaced by their genes.

autofit

If TRUE, we try to fit the edges to the labels. This is a very experimental feature, likely to be not very robust.

scale_char

If using autofit = TRUE, the scaling factor for the size of the rectangles as a function of the number of characters. You have to play with this because the best value can depend on a number of things.

return_g

It TRUE, the graph object (graphNEL or igrap) is returned.

lwdf

The multiplier factor for lwd when using "graphNEL".

...

Other arguments passed to plot. Not used for now.

Value

Order and epistatic relationships have orange edges. OR (semimonotone) relationships blue, and XOR red. All others have black edges (so AND and unique edges from root). Epistatic relationships, being symmetrical, have no arrows between nodes and have a dotted line type. Order relationships have an arrow from the earlier to the later event and have a different dotted line (lty 3).If return_g is TRUE, you are returned also the graph object (igraph or graphNEL) so that you can manipulate it further.

See Also

allFitnessEffects

Examples

cs <-  data.frame(parent = c(rep("Root", 4), "a", "b", "d", "e", "c"),
                 child = c("a", "b", "d", "e", "c", "c", rep("g", 3)),
                 s = 0.1,
                 sh = -0.9,
                 typeDep = "MN")

cbn1 <- allFitnessEffects(cs)
plot(cbn1, "igraph")

library(igraph) ## to make layouts available
plot(cbn1, "igraph", layout = layout.reingold.tilford)


### A DAG with the three types of relationships
p3 <- data.frame(parent = c(rep("Root", 4), "a", "b", "d", "e", "c", "f"),
                  child = c("a", "b", "d", "e", "c", "c", "f", "f", "g", "g"),
                  s = c(0.01, 0.02, 0.03, 0.04, 0.1, 0.1, 0.2, 0.2, 0.3, 0.3),
                  sh = c(rep(0, 4), c(-.9, -.9), c(-.95, -.95), c(-.99, -.99)),
                  typeDep = c(rep("--", 4), 
                      "XMPN", "XMPN", "MN", "MN", "SM", "SM"))
fp3 <- allFitnessEffects(p3)

plot(fp3)

plot(fp3, "igraph", layout = layout.reingold.tilford)


## A more complex example, that includes a restriction table
## order effects, epistasis, genes without interactions, and moduels
p4 <- data.frame(parent = c(rep("Root", 4), "A", "B", "D", "E", "C", "F"),
                 child = c("A", "B", "D", "E", "C", "C", "F", "F", "G", "G"),
                 s = c(0.01, 0.02, 0.03, 0.04, 0.1, 0.1, 0.2, 0.2, 0.3, 0.3),
                 sh = c(rep(0, 4), c(-.9, -.9), c(-.95, -.95), c(-.99, -.99)),
                 typeDep = c(rep("--", 4), 
                     "XMPN", "XMPN", "MN", "MN", "SM", "SM"))

oe <- c("C > F" = -0.1, "H > I" = 0.12)
sm <- c("I:J"  = -1)
sv <- c("-K:M" = -.5, "K:-M" = -.5)
epist <- c(sm, sv)

modules <- c("Root" = "Root", "A" = "a1",
             "B" = "b1, b2", "C" = "c1",
             "D" = "d1, d2", "E" = "e1",
             "F" = "f1, f2", "G" = "g1",
             "H" = "h1, h2", "I" = "i1",
             "J" = "j1, j2", "K" = "k1, k2", "M" = "m1")

noint <- rexp(5, 10)
names(noint) <- paste0("n", 1:5)

fea <- allFitnessEffects(rT = p4, epistasis = epist, orderEffects = oe,
                         noIntGenes = noint, geneToModule = modules)


plot(fea)
plot(fea, expandModules = TRUE)
plot(fea, type = "igraph")