GenVisR: Genomic Visualizations in R
Version 1.6.0

Produce highly customizable publication quality graphics for genomic data primarily at the cohort level.

Browse man pages Browse package API and functions Browse package files

AuthorZachary Skidmore [aut, cre], Alex Wagner [aut], Robert Lesurf [aut], Katie Campbell [aut], Jason Kunisaki [aut], Obi Griffith [aut], Malachi Griffith [aut]
Bioconductor views Classification DNASeq DataRepresentation Infrastructure
Date of publicationNone
MaintainerZachary Skidmore <zlskidmore@gmail.com>
LicenseGPL-3 + file LICENSE
Version1.6.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("GenVisR")

Man pages

brcaMAF: Truncated BRCA MAF file
cnFreq: Construct copy-number frequency plot
cnFreq_buildMain: Construct CN frequency plot
cnFreq_qual: check input to cnFreq
cnSpec: Construct copy-number cohort plot
cnSpec_buildMain: Construct CN cohort plot
cnSpec_qual: Construct CN cohort plot
cnView: Construct copy-number single sample plot
cnView_buildMain: construct CN plot
cnView_qual: check input to cnView
compIdent: Construct identity snp comparison plot
compIdent_bamRcnt: Count nucleotide reads at SNP locations
compIdent_bamRcnt_qual: Count nucleotide reads at SNP locations
compIdent_buildMain: Compare sample identities
compIdent_format: Format readcount tables from compIdent
covBars: Construct an overall coverage cohort plot
covBars_buildMain: Construct coverage cohort plot
covBars_qual: Construct coverage cohort plot
cytoGeno: Cytogenetic banding dataset
genCov: Construct a region of interest coverage plot
genCov_alignPlot: align plots on an axis
genCov_assign_ggplotGrob_height: assign ggplotGrob height
genCov_assign_ggplotGrob_width: assign ggplotGrob width
genCov_buildCov: build coverage plot
genCov_buildTrack: build label for plot
genCov_extr_ggplotGrob_height: extract ggplotGrob height
genCov_extr_ggplotGrob_width: extract ggplotGrob width
genCov_qual: Perform quality control on genCov data
genCov_trackViz: Overlay tracks with plots
geneViz: Construct a gene-features plot
geneViz_buildGene: build gene plot
geneViz_calcGC: Calculate GC content
geneViz_cdsFromTXID: cdsFromTXID
geneViz_extrCDS: Extract CDS
geneViz_extrUTR: Extract UTR
geneViz_formatCDS: format cds
geneViz_formatUTR: format UTR
geneViz_Granges2dataframe: Convert Granges object to dataframe
geneViz_mapCoordSpace: Map regions to transformed space
geneViz_mapCovCoordSpace: Map coverage track regions to transformed space
geneViz_mergeRegions: Create Region Table
geneViz_mergeTypeRegions: Create Typed Region Table
geneViz_mergeTypes: Merge Typed Region Tables
GenVisR: GenVisR
HCC1395_Germline: Germline Calls
HCC1395_N: Normal BAM
HCC1395_T: Tumor BAM
hg19chr: hg19 chromosome boundaries
ideoView: Construct an ideogram
ideoView_buildMain: build chromosome
ideoView_formatCytobands: reformat cytogenetic band data frame
ideoView_qual: Check input to ideoView
lohSpec: Plot LOH data
lohSpec_buildMain: Plot LOH data
lohSpec_fileGlob: Grab data for lohSpec
lohSpec_lohCalc: Calculate loh difference
lohSpec_qual: Check input to lohSpec
lohSpec_slidingWindow: Obtain LOH data
lohSpec_stepCalc: Obtain average loh within each step
lohSpec_tileCalc: Calculate loh difference
lohSpec_tilePosition: Obtain window information
lohSpec_tileWindow: Obtain LOH data
lohSpec_windowPosition: Obtain window information
lohView: Construct LOH chromosome plot
lohView_buildMain: construct loh plot
lohView_qual: check input to lohView
lolliplot: Construct a lolliplot
lolliplot_AA2sidechain: Convert AA to side chain classification
lolliplot_buildMain: Construct Lolliplot
lolliplot_Codon2AA: Convert Codon to AA
lolliplot_constructGene: Construct gene information
lolliplot_DNAconv: Convert DNA character string
lolliplot_dodgeCoordX: dodge coordinates
lolliplot_dodgeCoordY: dodge coordinates
lolliplot_fetchDomain: fetch protein domains
lolliplot_mutationObs: format mutation observations
lolliplot_qual: Check input to lolliplot
lolliplot_reduceLolli: Reduce Lolli
lolliplot_transcriptID2codingSeq: fetch protein length
LucCNseg: Truncated CN segments
multi_align: align CN/LOH plots on x axis
multi_buildClin: plot clinical information
multi_chrBound: retrieve and format CN_cohort plot supplemental data
multi_cytobandRet: Retrieve cytogenetic bands
multi_selectOut: Choose output
multi_subsetChr: subset based on chr
SNPloci: Identity snps
TvTi: Construct transition-transversion plot
TvTi_alignPlot: align TvTi plots on y axis
TvTi_annoTransTranv: Annotate Transitions and Transversions
TvTi_buildMain: build transitions/transversions
TvTi_calcTransTranvFreq: Calculate Transition/Transversion Frequency
TvTi_convMAF: Convert .maf format to internal format
TvTi_qual: Check input to TvTi
TvTi_rmIndel: Remove indels
TvTi_rmMnuc: Remove multinucleotide codes
waterfall: Construct a waterfall plot
waterfall_align: align plots
waterfall_buildGenePrevelance: plot mutation recurrence in genes
waterfall_buildMain: Plot a mutation heatmap
waterfall_buildMutBurden_A: plot mutation burden
waterfall_buildMutBurden_B: plot mutation burden
waterfall_build_proportions: Build mutational profile plot
waterfall_calcMutFreq: Calculate Synonymous/Nonsynonymous mutation frequency
waterfall_Custom2anno: Convert Custom File
waterfall_geneAlt: mutation sample cutoff gene based
waterfall_geneRecurCutoff: Mutation Recurrence Cutoff
waterfall_geneSort: sort waterfall file by gene
waterfall_hierarchyTRV: Hiearchical removal of MAF entries
waterfall_MAF2anno: Convert MAF File
waterfall_MGI2anno: Convert MGI File
waterfall_NA2gene: Assign NA samples a gene
waterfall_palette_names: waterfall_palette_names
waterfall_qual: Check input to mutSpec
waterfall_rmvSilent: Silent Mutation Removal
waterfall_sampAlt: mutation sample subset sample based
waterfall_sampSort: sort samples in an internal waterfall file.
waterfall_select_palette: Helper function to select a colour palette

Functions

GenVisR Man page
GenVisR-package Man page
HCC1395_Germline Man page
HCC1395_N Man page
HCC1395_T Man page
LucCNseg Man page
SNPloci Man page
TvTi Man page Source code
TvTi_alignPlot Man page Source code
TvTi_annoTransTranv Man page Source code
TvTi_buildMain Man page Source code
TvTi_calcTransTranvFreq Man page Source code
TvTi_convMAF Man page
TvTi_convMaf Man page Source code
TvTi_qual Man page Source code
TvTi_rmIndel Man page Source code
TvTi_rmMnuc Man page Source code
brcaMAF Man page
cnFreq Man page Source code
cnFreq_buildMain Man page Source code
cnFreq_disjoin Source code
cnFreq_qual Man page Source code
cnSpec Man page Source code
cnSpec_buildMain Man page Source code
cnSpec_qual Man page Source code
cnView Man page Source code
cnView_buildMain Man page Source code
cnView_qual Man page Source code
compIdent Man page Source code
compIdent_bamRcnt Man page Source code
compIdent_bamRcnt_qual Man page Source code
compIdent_buildMain Man page Source code
compIdent_format Man page Source code
covBars Man page Source code
covBars_buildMain Man page Source code
covBars_qual Man page Source code
cytoGeno Man page
genCov Man page Source code
genCov_alignPlot Man page Source code
genCov_assign_ggplotGrob_height Man page Source code
genCov_assign_ggplotGrob_width Man page Source code
genCov_buildCov Man page Source code
genCov_buildTrack Man page Source code
genCov_extr_ggplotGrob_height Man page Source code
genCov_extr_ggplotGrob_width Man page Source code
genCov_qual Man page Source code
genCov_trackViz Man page Source code
geneViz Man page Source code
geneViz_Granges2dataframe Man page Source code
geneViz_buildGene Man page Source code
geneViz_calcGC Man page Source code
geneViz_cdsFromTXID Man page Source code
geneViz_extrCDS Man page Source code
geneViz_extrUTR Man page Source code
geneViz_formatCDS Man page Source code
geneViz_formatUTR Man page Source code
geneViz_mapCoordSpace Man page Source code
geneViz_mapCovCoordSpace Man page Source code
geneViz_mergeRegions Man page Source code
geneViz_mergeTypeRegions Man page Source code
geneViz_mergeTypes Man page Source code
hg19chr Man page
ideoView Man page Source code
ideoView_buildMain Man page Source code
ideoView_formatCytobands Man page Source code
ideoView_qual Man page Source code
lohSpec Man page Source code
lohSpec_buildMain Man page Source code
lohSpec_fileGlob Man page Source code
lohSpec_lohCalc Man page Source code
lohSpec_qual Man page Source code
lohSpec_slidingWindow Man page Source code
lohSpec_stepCalc Man page Source code
lohSpec_tileCalc Man page Source code
lohSpec_tilePosition Man page Source code
lohSpec_tileWindow Man page Source code
lohSpec_windowPosition Man page Source code
lohView Man page Source code
lohView_buildMain Man page Source code
lohView_qual Man page Source code
lolliplot Man page Source code
lolliplot_AA2sidechain Man page Source code
lolliplot_Codon2AA Man page Source code
lolliplot_DNAconv Man page Source code
lolliplot_buildMain Man page Source code
lolliplot_constructGene Man page Source code
lolliplot_dodgeCoordX Man page Source code
lolliplot_dodgeCoordY Man page Source code
lolliplot_fetchDomain Man page Source code
lolliplot_mutationObs Man page Source code
lolliplot_qual Man page Source code
lolliplot_reduceLolli Man page Source code
lolliplot_transcriptID2codingSeq Man page Source code
multi_align Man page Source code
multi_buildClin Man page Source code
multi_chrBound Man page Source code
multi_cytobandRet Man page Source code
multi_selectOut Man page Source code
multi_subsetChr Man page Source code
waterfall Man page Source code
waterfall_Custom2anno Man page Source code
waterfall_MAF2anno Man page Source code
waterfall_MGI2anno Man page Source code
waterfall_NA2gene Man page Source code
waterfall_align Man page Source code
waterfall_buildGenePrevelance Man page Source code
waterfall_buildMain Man page Source code
waterfall_buildMutBurden_A Man page Source code
waterfall_buildMutBurden_B Man page Source code
waterfall_build_proportions Man page Source code
waterfall_calcMutFreq Man page Source code
waterfall_geneAlt Man page Source code
waterfall_geneRecurCutoff Man page Source code
waterfall_geneSort Man page Source code
waterfall_hierarchyTRV Man page Source code
waterfall_palette_names Man page Source code
waterfall_qual Man page Source code
waterfall_rmvSilent Man page Source code
waterfall_sampAlt Man page Source code
waterfall_sampSort Man page Source code
waterfall_select_palette Man page Source code

Files

DESCRIPTION
LICENSE
NAMESPACE
NEWS
R
R/GenVisR.R
R/TvTi.R
R/TvTi_alignPlot.R
R/TvTi_annoTransTranv.R
R/TvTi_buildMain.R
R/TvTi_calcTransTranvFreq.R
R/TvTi_convMaf.R
R/TvTi_qual.R
R/TvTi_rmIndel.R
R/TvTi_rmMnuc.R
R/cnFreq.R
R/cnFreq_buildMain.R
R/cnFreq_disjoin.R
R/cnFreq_qual.R
R/cnSpec.R
R/cnSpec_buildMain.R
R/cnSpec_qual.R
R/cnView.R
R/cnView_buildMain.R
R/cnView_qual.R
R/compIdent.R
R/compIdent_bamRcnt.R
R/compIdent_bamRcnt_qual.R
R/compIdent_buildMain.R
R/compIdent_format.R
R/covBars.R
R/covBars_buildMain.R
R/covBars_qual.R
R/genCov.R
R/genCov_alignPlot.R
R/genCov_assign_ggplotGrob_height.R
R/genCov_assign_ggplotGrob_width.R
R/genCov_buildCov.R
R/genCov_buildTrack.R
R/genCov_extr_ggplotGrob_height.R
R/genCov_extr_ggplotGrob_width.R
R/genCov_qual.R
R/genCov_trackViz.R
R/geneViz.R
R/geneViz_Granges2dataframe.R
R/geneViz_buildGene.R
R/geneViz_calcGC.R
R/geneViz_cdsFromTXID.R
R/geneViz_extrCDS.R
R/geneViz_extrUTR.R
R/geneViz_formatUTR.R
R/geneViz_formatcds.R
R/geneViz_mapCoordSpace.R
R/geneViz_mapCovCoordSpace.R
R/geneViz_mergeRegions.R
R/geneViz_mergeTypeRegions.R
R/geneViz_mergeTypes.R
R/ideoView.R
R/ideoView_buildMain.R
R/ideoView_formatCytobands.R
R/ideoView_qual.R
R/lohSpec.R
R/lohSpec_buildMain.R
R/lohSpec_fileGlob.R
R/lohSpec_lohCalc.R
R/lohSpec_qual.R
R/lohSpec_slidingWindow.R
R/lohSpec_stepCalc.R
R/lohSpec_tileCalc.R
R/lohSpec_tilePosition.R
R/lohSpec_tileWindow.R
R/lohSpec_windowPosition.R
R/lohView.R
R/lohView_buildMain.R
R/lohView_qual.R
R/lolliplot.R
R/lolliplot_AA2sidechain.R
R/lolliplot_Codon2AA.R
R/lolliplot_DNAconv.R
R/lolliplot_buildMain.R
R/lolliplot_constructGene.R
R/lolliplot_dodgeCoordX.R
R/lolliplot_dodgeCoordY.R
R/lolliplot_fetchDomain.R
R/lolliplot_mutationObs.R
R/lolliplot_qual.R
R/lolliplot_reduceLolli.R
R/lolliplot_transcriptID2codingSeq.R
R/multi_align.R
R/multi_buildClin.R
R/multi_chrBound.R
R/multi_cytobandRet.R
R/multi_selectOut.R
R/multi_subsetChr.R
R/waterfall.R
R/waterfall_Custom2anno.R
R/waterfall_MAF2anno.R
R/waterfall_MGI2anno.R
R/waterfall_NA2gene.R
R/waterfall_align.R
R/waterfall_buildGenePrevelance.R
R/waterfall_buildMain.R
R/waterfall_buildMutBurden_A.R
R/waterfall_buildMutBurden_B.R
R/waterfall_build_proportions.R
R/waterfall_calcMutFreq.R
R/waterfall_geneAlt.R
R/waterfall_geneRecurCutoff.R
R/waterfall_geneSort.R
R/waterfall_hierarchyTRV.R
R/waterfall_palette_names.R
R/waterfall_qual.R
R/waterfall_rmvSilent.R
R/waterfall_sampAlt.R
R/waterfall_sampSort.R
R/waterfall_select_palette.R
README.md
build
build/vignette.rds
data
data/HCC1395_Germline.rda
data/HCC1395_N.rda
data/HCC1395_T.rda
data/LucCNseg.rda
data/SNPloci.rda
data/brcaMAF.rda
data/cytoGeno.rda
data/hg19chr.rda
inst
inst/CITATION
inst/doc
inst/doc/GenVisR_intro.R
inst/doc/GenVisR_intro.Rmd
inst/doc/GenVisR_intro.html
inst/doc/waterfall_introduction.R
inst/doc/waterfall_introduction.Rmd
inst/doc/waterfall_introduction.html
man
man/GenVisR.Rd
man/HCC1395_Germline.Rd
man/HCC1395_N.Rd
man/HCC1395_T.Rd
man/LucCNseg.Rd
man/SNPloci.Rd
man/TvTi.Rd
man/TvTi_alignPlot.Rd
man/TvTi_annoTransTranv.Rd
man/TvTi_buildMain.Rd
man/TvTi_calcTransTranvFreq.Rd
man/TvTi_convMAF.Rd
man/TvTi_qual.Rd
man/TvTi_rmIndel.Rd
man/TvTi_rmMnuc.Rd
man/brcaMAF.Rd
man/cnFreq.Rd
man/cnFreq_buildMain.Rd
man/cnFreq_qual.Rd
man/cnSpec.Rd
man/cnSpec_buildMain.Rd
man/cnSpec_qual.Rd
man/cnView.Rd
man/cnView_buildMain.Rd
man/cnView_qual.Rd
man/compIdent.Rd
man/compIdent_bamRcnt.Rd
man/compIdent_bamRcnt_qual.Rd
man/compIdent_buildMain.Rd
man/compIdent_format.Rd
man/covBars.Rd
man/covBars_buildMain.Rd
man/covBars_qual.Rd
man/cytoGeno.Rd
man/genCov.Rd
man/genCov_alignPlot.Rd
man/genCov_assign_ggplotGrob_height.Rd
man/genCov_assign_ggplotGrob_width.Rd
man/genCov_buildCov.Rd
man/genCov_buildTrack.Rd
man/genCov_extr_ggplotGrob_height.Rd
man/genCov_extr_ggplotGrob_width.Rd
man/genCov_qual.Rd
man/genCov_trackViz.Rd
man/geneViz.Rd
man/geneViz_Granges2dataframe.Rd
man/geneViz_buildGene.Rd
man/geneViz_calcGC.Rd
man/geneViz_cdsFromTXID.Rd
man/geneViz_extrCDS.Rd
man/geneViz_extrUTR.Rd
man/geneViz_formatCDS.Rd
man/geneViz_formatUTR.Rd
man/geneViz_mapCoordSpace.Rd
man/geneViz_mapCovCoordSpace.Rd
man/geneViz_mergeRegions.Rd
man/geneViz_mergeTypeRegions.Rd
man/geneViz_mergeTypes.Rd
man/hg19chr.Rd
man/ideoView.Rd
man/ideoView_buildMain.Rd
man/ideoView_formatCytobands.Rd
man/ideoView_qual.Rd
man/lohSpec.Rd
man/lohSpec_buildMain.Rd
man/lohSpec_fileGlob.Rd
man/lohSpec_lohCalc.Rd
man/lohSpec_qual.Rd
man/lohSpec_slidingWindow.Rd
man/lohSpec_stepCalc.Rd
man/lohSpec_tileCalc.Rd
man/lohSpec_tilePosition.Rd
man/lohSpec_tileWindow.Rd
man/lohSpec_windowPosition.Rd
man/lohView.Rd
man/lohView_buildMain.Rd
man/lohView_qual.Rd
man/lolliplot.Rd
man/lolliplot_AA2sidechain.Rd
man/lolliplot_Codon2AA.Rd
man/lolliplot_DNAconv.Rd
man/lolliplot_buildMain.Rd
man/lolliplot_constructGene.Rd
man/lolliplot_dodgeCoordX.Rd
man/lolliplot_dodgeCoordY.Rd
man/lolliplot_fetchDomain.Rd
man/lolliplot_mutationObs.Rd
man/lolliplot_qual.Rd
man/lolliplot_reduceLolli.Rd
man/lolliplot_transcriptID2codingSeq.Rd
man/multi_align.Rd
man/multi_buildClin.Rd
man/multi_chrBound.Rd
man/multi_cytobandRet.Rd
man/multi_selectOut.Rd
man/multi_subsetChr.Rd
man/waterfall.Rd
man/waterfall_Custom2anno.Rd
man/waterfall_MAF2anno.Rd
man/waterfall_MGI2anno.Rd
man/waterfall_NA2gene.Rd
man/waterfall_align.Rd
man/waterfall_buildGenePrevelance.Rd
man/waterfall_buildMain.Rd
man/waterfall_buildMutBurden_A.Rd
man/waterfall_buildMutBurden_B.Rd
man/waterfall_build_proportions.Rd
man/waterfall_calcMutFreq.Rd
man/waterfall_geneAlt.Rd
man/waterfall_geneRecurCutoff.Rd
man/waterfall_geneSort.Rd
man/waterfall_hierarchyTRV.Rd
man/waterfall_palette_names.Rd
man/waterfall_qual.Rd
man/waterfall_rmvSilent.Rd
man/waterfall_sampAlt.Rd
man/waterfall_sampSort.Rd
man/waterfall_select_palette.Rd
tests
tests/testthat
tests/testthat.R
tests/testthat/test-TvTi.R
tests/testthat/test-TvTi_calcTransTranvFreq.R
tests/testthat/test-TvTi_convMaf.R
tests/testthat/test-TvTi_qual.R
tests/testthat/test-TvTi_rmIndel.R
tests/testthat/test-TvTi_rmMnuc.R
tests/testthat/test-cnSpec.R
tests/testthat/test-cnSpec_qual.R
tests/testthat/test-cnView_qual.R
tests/testthat/test-genCov_qual.R
tests/testthat/test-ideoView_formatCytobands.R
tests/testthat/test-lolliplot_AA2sidechain.R
tests/testthat/test-lolliplot_Codon2AA.R
tests/testthat/test-lolliplot_DNAconv.R
tests/testthat/test-lolliplot_constructGene.R
tests/testthat/test-lolliplot_dodgeCoordX.R
tests/testthat/test-lolliplot_dodgeCoordY.R
tests/testthat/test-lolliplot_mutationObs.R
tests/testthat/test-lolliplot_qual.R
tests/testthat/test-lolliplot_reduceLolli.R
tests/testthat/test-multi_chrBound.R
tests/testthat/test-multi_cytobandRet.R
tests/testthat/test-multi_subsetChr.R
tests/testthat/test-waterfall.R
tests/testthat/test-waterfall_MAF2anno.R
tests/testthat/test-waterfall_MGI2anno.R
tests/testthat/test-waterfall_NA2gene.R
tests/testthat/test-waterfall_calcMutFreq.R
tests/testthat/test-waterfall_geneAlt.R
tests/testthat/test-waterfall_geneRecurCutoff.R
tests/testthat/test-waterfall_geneSort.R
tests/testthat/test-waterfall_qual.R
tests/testthat/test-waterfall_rmvSilent.R
tests/testthat/test-waterfall_sampAlt.R
tests/testthat/test-waterfall_sampSort.R
tests/testthat/test_waterfall_hierarchyTRV.R
vignettes
vignettes/GenVisR_intro.Rmd
vignettes/waterfall_introduction.Rmd
GenVisR documentation built on May 20, 2017, 10:10 p.m.