Introduction | To install: | Using CRAN | Input files | Alignment output file format for reformat.syntenyData() function | Example file format | Alignment file input format for draw.eh(), draw.ideogram(), and draw.linear() functions | Chromosome Length file for draw.ideogram() and draw.linear() functions | Reformatting alignment data | Usage | Example code using data files in inst/extdata/ | Evolution Highway style | Example output: | Chromosome painting style | Linear style
Package: syntenyPlotteR 1.0.0
Marta Farre
syntenyPlotteR: Genome Synteny Visualization
Draw syntenic relationships between genome assemblies. There are 3 functions which take a tab delimited file containing alignment data for syntenic blocks between genomes to produce either a linear alignment plot, an evolution highway style plot, or a painted ideogram representing syntenic relationships. There is also a function to convert alignment data in the DESCHRAMBLER/inferCAR format to the required data structure.
Authors:
syntenyPlotteR_1.0.0.tar.gz
syntenyPlotteR_1.0.0.zip(r-4.7-any)syntenyPlotteR_1.0.0.zip(r-4.6-any)syntenyPlotteR_1.0.0.zip(r-4.5-any)
syntenyPlotteR_1.0.0.tgz(r-4.6-any)syntenyPlotteR_1.0.0.tgz(r-4.5-any)
syntenyPlotteR_1.0.0.tar.gz(r-4.7-any)syntenyPlotteR_1.0.0.tar.gz(r-4.6-any)
syntenyPlotteR_1.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
syntenyPlotteR/json (API)
| # Install 'syntenyPlotteR' in R: |
| install.packages('syntenyPlotteR', repos = c('https://farre-lab.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/farre-lab/syntenyplotter/issues
Pkgdown/docs site:https://farre-lab.github.io
Last updated from:5dd36b9bcd. Checks:7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | NOTE | 143 | ||
| source / vignettes | OK | 165 | ||
| linux-release | NOTE | 140 | ||
| macos-release | NOTE | 155 | ||
| macos-oldrel | NOTE | 131 | ||
| windows-devel | NOTE | 73 | ||
| windows-release | NOTE | 104 | ||
| windows-oldrel | NOTE | 80 | ||
| wasm-release | OK | 123 |
Exports:draw.ehdraw.ideogramdraw.linearreformat.syntenyData
Dependencies:clicpp11farverggplot2gluegtableisobandlabelinglifecyclemagrittrR6RColorBrewerrlangS7scalesstringistringrvctrsviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Evolution Highway style plot | draw.eh |
| Draw ideograms in chromosome painting style | draw.ideogram |
| Linear synteny plot | draw.linear |
| Reformat synteny data | reformat.syntenyData |