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])

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 comrelling. To use this interactively with TCGA, contact the ISB and obtain a cloud platform account. Then obtain the cgcR package, load it, and run isbApp(). You will have to authenticate with google to get access to the BigQuery representation of TCGA.

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 interacts with the epiviz system and is capable of substantial feats of data integration and higher-level data interactivity.