GenVisR: Genomic Visualizations in R

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

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("GenVisR")
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
Version1.4.1

View on Bioconductor

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

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

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_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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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All documentation is copyright its authors; we didn't write any of that.