Some final comments on genome-scale visualization
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]
## $$rs10484554 ##  "TMEM154" "CDC42EP4" "LRBA" "AE000660.1-5" ##  "U66060.1-23" ## ## $$rs10484561 ##  "LIMS1" "U66060.1-23" "AE000660.1-4" "CD19" ##  "FCRLA" "CD79B" "ERG" ## ## $$rs10758658 ##  "TSTA3" "BCL2L1" "AC010679.1" "SIAH2" "EPB41" ##  "ECM2"
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.