R: Venn Diagrams

venn {limma}

R Documentation

Venn Diagrams

Description

Compute classification counts or plot classification counts in a Venn diagram.

Usage

vennCounts(x, include="both")
vennDiagram(object, include="both", names, mar=rep(1,4), cex=1.5, lwd=1,
circle.col, counts.col, show.include, ...)

Arguments

`x`	numeric matrix of 0's and 1's indicating significance of a test. Usually created by `decideTests`.
`object`	either a `TestResults` matrix or a `VennCounts` object produced by `vennCounts`.
`include`	character string, of length one or two, specifying whether the diagram should give counts for genes up-regulated, down-regulated or both. See details. Choices are `"both"`, `"up"` or `"down"`.
`names`	optional character vector giving names for the sets or contrasts
`mar`	numeric vector of length 4 specifying the width of the margins around the plot. This argument is passed to `par`.
`cex`	numerical value giving the amount by which the contrast names should be scaled on the plot relative to the default.plotting text. See `par`.
`lwd`	numerical value giving the amount by which the circles should be scaled on the plot. See `par`.
`circle.col`	optional vector of color specifications defining the colors by which the circles should be drawn. See `par`.
`counts.col`	optional vector of color specifications, of same length as `include`, defining the colors by which the counts should be drawn. See `par`.
`show.include`	logical value whether the value of `include` should be printed on the plot. Defaults to `FALSE` if `include` is a single value and `TRUE` otherwise
`...`	any other arguments are passed to `plot`

Details

If a vennCounts object is given to vennDiagram, the include parameter is ignored. If a TestResults object is given, then it is possible to set include as a vector of 2 character strings and both will be shown.

Value

vennCounts produces a VennCounts object, which is a numeric matrix with last column "Counts" giving counts for each possible vector outcome. vennDiagram causes a plot to be produced on the current graphical device. For venDiagram, the number of columns of object should be three or fewer.

Author(s)

Gordon Smyth, James Wettenhall and Francois Pepin

Examples

Y <- matrix(rnorm(100*6),100,6)
Y[1:10,3:4] <- Y[1:10,3:4]+3
Y[1:20,5:6] <- Y[1:20,5:6]+3
design <- cbind(1,c(0,0,1,1,0,0),c(0,0,0,0,1,1))
fit <- eBayes(lmFit(Y,design))
results <- decideTests(fit)
a <- vennCounts(results)
print(a)
vennDiagram(a)
vennDiagram(results,include=c("up","down"),counts.col=c("red","green"))

[Package limma version 3.10.2 Index]