| venn {limma} | R Documentation |
Compute classification counts or plot classification counts in a Venn diagram.
vennCounts(x, include="both") vennDiagram(object, include="both", names, mar=rep(1,4), cex=1.5, ...)
x |
numeric matrix of 0's and 1's indicating significance of a test.
Usually created by decideTests or classifyTests. |
object |
either a TestResults matrix or a VennCounts object produced by vennCounts. |
include |
character string specifying whether to counts genes up-regulated, down-regulated or both.
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. |
... |
any other arguments are passed to plot |
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.
Gordon Smyth and James Wettenhall
An overview of linear model functions in limma is given by 5.LinearModels.
tstat <- matrix(rt(300,df=10),100,3) tstat[1:33,] <- tstat[1:33,]+2 clas <- classifyTestsF(tstat,df=10,p.value=0.05) a <- vennCounts(clas) print(a) vennDiagram(a)