venn: Venn Diagrams
In richierocks/limma2: Linear Models for Microarray Data

Description Usage Arguments Details Value Author(s) See Also Examples

Compute Classification Counts and Make Venn Diagram.

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vennCounts(x, include="both")
vennDiagram(object, include="both", names=NULL, mar=rep(1,4), cex=c(1.5,1,0.7), lwd=1,
            circle.col=NULL, counts.col=NULL, show.include=NULL, ...)

`x`	numeric matrix of 0's and 1's indicating significance of a test. Usually created by `decideTests`.
`object`	either a `TestResults` matrix from `decideTests` or a `VennCounts` object produced by `vennCounts`.
`include`	character vector specifying whether all differentially expressed genes should be counted, or whether the counts should be restricted to genes changing in a certain direction. Choices are `"both"` for all differentially expressed genes, `"up"` for up-regulated genes only or `"down"` for down-regulated genes only. If `include=c("up","down")` then both the up and down counts will be shown. This argument is ignored if `object` if `object` is already a `vennCounts` object.
`names`	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 vector of length 3 giving scaling factors for large, medium and small text on the plot.
`lwd`	numerical value giving the amount by which the circles should be scaled on the plot. See `par`.
`circle.col`	vector of color specifications defining the colors by which the circles should be drawn. See `par`.
`counts.col`	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`

vennDiagram can plot up to five sets. vennCounts can collate intersection counts for any number of sets.

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.

Gordon Smyth, James Wettenhall, Francois Pepin, Steffen Moeller and Yifang Hu

An overview of linear model functions in limma is given by 06.LinearModels.

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)
mfrow.old <- par()$mfrow
par(mfrow=c(1,2))
vennDiagram(a)
vennDiagram(results,include=c("up","down"),counts.col=c("red","green"))
par(mfrow=mfrow.old)