RCircos

RCircos is not distributed in Bioconductor, but can be useful for developing compact displays of interactions among genomic elements. I am unaware of any interfaces between Bioconductor data classes and RCircos, and this topic deserves attention.

In the ph525x package we have added a selection of trans-eQTL findings from Westra et al. Nature 2013 (doi: 10.1038/ng.2756). We show a few SNP-gene associations from this study:

library(ph525x)
data(westraTransSel)
westraTransSel[1:3]
## $$rs10484554
## [1] "TMEM154"      "CDC42EP4"     "LRBA"         "AE000660.1-5"
## [5] "U66060.1-23" 
## 
## $$rs10484561
## [1] "LIMS1"        "U66060.1-23"  "AE000660.1-4" "CD19"        
## [5] "FCRLA"        "CD79B"        "ERG"         
## 
## $$rs10758658
## [1] "TSTA3"      "BCL2L1"     "AC010679.1" "SIAH2"      "EPB41"     
## [6] "ECM2"
sglToCircos(westraTransSel[1:5])
## Loading required package: SNPlocs.Hsapiens.dbSNP144.GRCh37
## Loading required package: BSgenome
## Loading required package: Biostrings
## Loading required package: XVector
## Loading required package: rtracklayer
## 'select()' returned 1:1 mapping between keys and columns
## 'select()' returned 1:1 mapping between keys and columns
## 'select()' returned 1:1 mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns
## Some chromosomes are in genomic data only and have been removed.
## 
## 'select()' returned 1:1 mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns
## 
## Maximum lables for  chr20 is 2 .
## Extra ones are ignored.
## 

plot of chunk lksn

ComplexHeatmap

ComplexHeatmap has a very nice vignette addressing many issues in combining heatmaps and repurposing the heatmap concept. The oncoprint example in the vignette is particularly compelling.

WebGL and interaction with data

In the short concluding video we use the MLInterfaces plspinHcube function to illustrate several aspects of interactivity: GUI for tuning, mouse-controlled rotation, and mouseover for point interrogation.

EpiViz

The epivizr package is capable of substantial feats of data integration and higher-level data interactivity.