Tool: GenVisR: Genomic Visualizations in R
gravatar for Obi Griffith
4.0 years ago by
Obi Griffith18k
Washington University, St Louis, USA
Obi Griffith18k wrote:

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:

GenVisR sample figures

ADD COMMENTlink modified 12 months ago by abio0 • written 4.0 years ago by Obi Griffith18k

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.

ADD REPLYlink modified 3.8 years ago • written 3.8 years ago by oalder0

@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()

ADD REPLYlink written 3.1 years ago by zlskidmore290

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

ADD REPLYlink written 12 months ago by abio0
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