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)
