Venn Diagrams

source("http://faculty.ucr.edu/~tgirke/Documents/R_BioCond/My_R_Scripts/overLapper.R")
setlist5 <- list(A=sample(letters, 18), B=sample(letters, 16), C=sample(letters, 20), D=sample(letters, 22), E=sample(letters, 18))
OLlist5 <- overLapper(setlist=setlist5, sep="_", type="vennsets")
counts <- sapply(OLlist5$Venn_List, length)
vennPlot(counts=counts, ccol=c(rep(1,30),2), lcex=1.5, ccex=c(rep(1.5,5), rep(0.6,25),1.5))

Compound Structures

Plots depictions of small molecules with ChemmineR package

library(ChemmineR)
## 
## Attaching package: 'ChemmineR'
## The following object is masked from 'package:ShortRead':
## 
##     view
## The following object is masked from 'package:S4Vectors':
## 
##     fold
data(sdfsample)
plot(sdfsample[1], print=FALSE)

ROC Plots

A variety of libraries are available for plotting receiver operating characteristic (ROC) curves in R:

Trees

The ape package provides many useful utilities for phylogenetic analysis and tree plotting. Another useful package for plotting trees is ggtree. The following example plots two trees face to face with links to identical leaf labels.

library(ape)
tree1 <- rtree(40)
tree2 <- rtree(20)
association <- cbind(tree2$tip.label, tree2$tip.label)
cophyloplot(tree1, tree2, assoc = association,
            length.line = 4, space = 28, gap = 3)