group.venn: Plot Venn Diagram For Two To Five Sets With Item Labels

In RAM: R for Amplicon-Sequencing-Based Microbial-Ecology

Description

This function use draw.pairwise.venn to creates a venn diagram for two vectors

Usage

group.venn(vectors, cat.cex=1.5, cex=1,
           cat.pos=NULL, cat.dist=NULL,
           label=TRUE, lab.cex=1,
           lab.col= "black", fill=NULL,
           file=NULL, ext=NULL, width=8, height=8)

Arguments

vectors	a list of vectors with names. See also RAM.input.formatting.
cat.cex	size of the category names. (see venn.diagram for details).
cex	size of the label of the circles. (see venn.diagram for details).
cat.pos	optional. Location of the category names along the circles. (see venn.diagram for details).
cat.dist	optional. Distance of the category names to the circles. (see venn.diagram for details).
label	logical. If TRUE, will plot the item labels for 2 data sets. For more than 2 datasets or this is set as FALSE, the labels will be numbers for each circle. (see venn.diagram for details).
lab.cex	size of the labels.
lab.col	color of the labels.
fill	optional, color of the circles. (see venn.diagram for details).
file	the file path where the image should be created (see ?RAM.plotting).
ext	filename extension, the type of image to be saved to.
height	the height of the image to be created (in inches).
width	the width of the image to be created (in inches).

Value

group.venn returns a venn diagram for 2 to 5 sets. The user can choose to place item labels for 2 sets of data, however, the label locations can be wrong if the the smaller data set is part of the bigger data set, in this case, set label as FALSE. If the input datasets is more than 2, label will be ignored.

Author(s)

Wen Chen

See Also

see venn.diagram

Examples

data(ITS1, meta)
# core OTUs
core <- core.OTU.rank(data=list(ITS1=ITS1), meta=meta, rank="g",
                     meta.factor="Crop", percent=1)
# taxa that core OTUs assigned to
core.Crop1 <- core$ITS1$Crop1$taxa
core.Crop2 <- core$ITS1$Crop2$taxa
# venn plot
vectors <- list(Core_Crop1=core.Crop1, Core_Crop2=core.Crop2)
group.venn(vectors=vectors, label=TRUE, cat.pos=c(330, 150),
           lab.cex=0.7)
## Not run: 
group.venn(vectors=vectors, label=FALSE, cat.pos=c(330, 150),
           lab.cex=0.7, cex=3)

## End(Not run)

Example output

Loading required package: vegan
Loading required package: permute
Loading required package: lattice
This is vegan 2.4-4
Loading required package: ggplot2
sh: 1: cannot create /dev/null: Permission denied
sh: 1: cannot create /dev/null: Permission denied

RAM documentation built on May 2, 2019, 3:04 p.m.