Introduction | How to read Circos plots | Installation | Bioconductor | GitHub | R package dependencies | Quick start | Higher-level plotting steps | Insertion diagram | Alternate styles | Multiple insertion sites | Adding more information | How to set either_side | Plotting many insertions throughout the genome | Customising your multiple insertion diagram | Feature diagram | Plasmid map | Insertion of a complex construct | Session Info | References
Package: gmoviz 1.25.0
Kathleen Zeglinski
gmoviz: Seamless visualization of complex genomic variations in GMOs and edited cell lines
Genetically modified organisms (GMOs) and cell lines are widely used models in all kinds of biological research. As part of characterising these models, DNA sequencing technology and bioinformatics analyses are used systematically to study their genomes. Therefore, large volumes of data are generated and various algorithms are applied to analyse this data, which introduces a challenge on representing all findings in an informative and concise manner. `gmoviz` provides users with an easy way to visualise and facilitate the explanation of complex genomic editing events on a larger, biologically-relevant scale.
Authors:
gmoviz_1.25.0.tar.gz
gmoviz_1.25.0.zip(r-4.7-any)gmoviz_1.25.0.zip(r-4.6-any)gmoviz_1.25.0.zip(r-4.5-any)
gmoviz_1.25.0.tgz(r-4.6-any)gmoviz_1.25.0.tgz(r-4.5-any)
gmoviz_1.25.0.tar.gz(r-4.7-any)gmoviz_1.25.0.tar.gz(r-4.6-any)
gmoviz_1.25.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
gmoviz/json (API)
| # Install 'gmoviz' in R: |
| install.packages('gmoviz', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- bright_colours_opaque - Gmoviz colour sets
- bright_colours_transparent - Gmoviz colour sets
- nice_colours - Gmoviz colour sets
- pastel_colours - Gmoviz colour sets
- rich_colours - Gmoviz colour sets
On BioConductor:gmoviz-1.25.0(bioc 3.24)gmoviz-1.24.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
visualizationsequencinggeneticvariabilitygenomicvariationcoverage
Last updated from:3d7f727b7e. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 175 | ||
| linux-devel | NOTE | 383 | ||
| source / vignettes | OK | 267 | ||
| linux-release | NOTE | 340 | ||
| macos-release | NOTE | 232 | ||
| macos-oldrel | NOTE | 260 | ||
| windows-devel | NOTE | 243 | ||
| windows-release | NOTE | 232 | ||
| windows-oldrel | NOTE | 205 | ||
| wasm-release | OK | 150 |
Exports:drawFeatureTrackdrawLinegraphTrackdrawScatterplotTrackfeatureDiagramgetCoveragegetFeaturesgetIdeogramDatagetLabelsgmovizInitialisegmovizPlotinsertionDiagrammakeLegendsmultipleInsertionDiagram
Dependencies:AnnotationDbiaskpassBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobcachemcigarillocirclizecliclueclustercodetoolscolorspaceComplexHeatmapcpp11crayoncurlDBIdigestdoParallelfastmapforeachformatRfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicFeaturesGenomicRangesGetoptLongGlobalOptionsgluegridBasehttrIRangesiteratorsjsonliteKEGGRESTlambda.rlifecyclematrixStatsmemoisemimeopensslpkgconfigpngpracmaR6RColorBrewerRCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4VectorsSeqinfoshapesnowsysvctrsXMLXVectoryaml
gmoviz: seamless visualisation of complex genomic variations in GMOs and edited cell lines – An overview
Last update: 2025-07-23
Started: 2020-01-31
gmoviz: seamless visualisation of complex genomic variations in GMOs and edited cell lines – Advanced usage
Introduction | Incremental plotting steps | Dataset | Initialisation & Ideograms | Reading in the ideogram data | Filtering ideogram data | Initialising the graph | 'Coverage rectangles' | Reading in coverage data | Plotting coverage | Smoothing and windowing coverage data | Adding labels | Changing sector sizes | Setting custom sector widths | Zooming | Adding tracks | Feature track | Reading in the feature data | Adding a feature track | Label plotting and cutoffs for features | Numeric data tracks | Finishing touches | Legends | Arranging legends alongside plots | Other features and hints | gmoviz colour sets | Adding to plots using circlize functions | Session Info | References
Last update: 2020-04-01
Started: 2020-02-17
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| gmoviz colour sets | bright_colours_opaque bright_colours_transparent colourSets nice_colours pastel_colours rich_colours |
| Add a 'feature' track to an existing plot | drawFeatureTrack |
| Add a line graph track to an existing plot | drawLinegraphTrack |
| Add a scatterplot track to an existing plot | drawScatterplotTrack |
| Display 'features' of interest in a diagram | featureDiagram |
| Import coverage data from .bam file | getCoverage |
| Generate a GRanges containing 'features' from .gff files | getFeatures |
| Import transgenic genome data from .bam or .fasta file | getIdeogramData |
| Generate a GRanges of labels from .gff files | getLabels |
| Initialise the layout of the circular plot | gmovizInitialise |
| Generate an entire circular plot | gmovizPlot |
| Display number of copies of an insertion | insertionDiagram |
| Add a legend | makeLegends |
| Display multiple insertion events around a genome | multipleInsertionDiagram |