Tool:GenVisR: Genomic Visualizations in R

Question

[Obi Griffith]

Intuitively visualizing and interpreting data from high-throughput genomic technologies continues to be challenging. "Genomic Visualizations in R" (GenVisR) attempts to alleviate this burden by providing highly customizable publication-quality graphics supporting multiple species and focused primarily on a cohort level (i.e., multiple samples/patients). GenVisR attempts to maintain a high degree of flexibility while leveraging the abilities of ggplot2 and bioconductor to achieve this goal.

Please cite:

Skidmore ZL, Wagner AH, Lesurf R, Campbell KM, Kunisaki J, Griffith OL, Griffith M. 2016. GenVisR: Genomic Visualizations in R. Bioinformatics. pii: btw325. [Epub ahead of print]

PubMed | Bioinformatics Journal | BioRxiv | Bioconductor | GitHub

The following functions are available:

• lolliplot - Visualize mutation distributions (hotspots) for a gene across a cohort (panel A below)
• waterfall - Visualize a mutation landscape across a cohort (panel B below)
• genCov - Visualize sequence coverage across a specified region for a sample (panel C below)
• TvTi - Visualize transition/transversion spectrum across a cohort
• cnSpec - Visualize copy number variations (CNV) across a cohort
• cnView - Visualize individual copy number variations (CNV)
• cnFreq - Visualize frequencies of copy number variations (CNV) across a cohort
• ideoView - Create an ideogram graphic
• lohSpec - Visualize loss of heterozygosity (LOH) across a cohort (panel D below)
• lohView - Visualize individual loss of heterozygosity (LOH) events
• covBars - Visualize sequence coverage across a cohort (panel E below)
• compIdent - Confirm sample identities/mix-ups (panel F below)
• geneViz - Create a transcript representation

GenVisR Tutorials currently available at BioStars:

• How to create a mutation landscape (waterfall) plot with GenVisR
• How to create a mutation lolliplot with GenVisR

[oalder]

Thanks, the package is extremely useful.

I'm having trouble making a few of the waterfall functions work. eg.

waterfall_calcMutFreq(brcaMAF) Error: could not find function "waterfall_calcMutFreq" waterfall_buildMutBurden_A(brcaMAF) Error: could not find function "waterfall_buildMutBurden_A"

while in the same R studio ( session on OS

waterfall(brcaMAF, mainRecurCutoff = 0.1)

is working well.

[zlskidmore]

@oalder, those functions referenced above are internal GenVisR functions used by waterfall(), they really shouldn't even be in the reference manual they are mostly there for development notes (docs are autogenerated). I'll hide these in the next major release. However if you wanted to access them use a triple colon waterfall:::waterfall_calcMutFreq()

[abio]

Does GenVisR work with CNVkit structural variant cns, cnr and vcf files?