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 )