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)