Package: macrosyntR 0.3.4
macrosyntR: Draw Ordered Oxford Grids
Use standard genomics file format (BED) and a table of orthologs to illustrate synteny conservation at the genome-wide scale. Significantly conserved linkage groups are identified as described in Simakov et al. (2020) <doi:10.1038/s41559-020-1156-z> and displayed on an Oxford Grid (Edwards (1991) <doi:10.1111/j.1469-1809.1991.tb00394.x>) or a chord diagram as in Simakov et al. (2022) <doi:10.1126/sciadv.abi5884>. The package provides a function that uses a network-based greedy algorithm to find communities (Clauset et al. (2004) <doi:10.1103/PhysRevE.70.066111>) and so automatically order the chromosomes on the plot to improve interpretability.
Authors:
macrosyntR_0.3.4.tar.gz
macrosyntR_0.3.4.zip(r-4.5)macrosyntR_0.3.4.zip(r-4.4)macrosyntR_0.3.4.zip(r-4.3)
macrosyntR_0.3.4.tgz(r-4.4-any)macrosyntR_0.3.4.tgz(r-4.3-any)
macrosyntR_0.3.4.tar.gz(r-4.5-noble)macrosyntR_0.3.4.tar.gz(r-4.4-noble)
macrosyntR_0.3.4.tgz(r-4.4-emscripten)macrosyntR_0.3.4.tgz(r-4.3-emscripten)
macrosyntR.pdf |macrosyntR.html✨
macrosyntR/json (API)
NEWS
# Install 'macrosyntR' in R: |
install.packages('macrosyntR', repos = c('https://samilhll.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/samilhll/macrosyntr/issues
bioinformaticsgenomic-visualizationsgenomics
Last updated 5 months agofrom:a86189db19. Checks:OK: 7. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Nov 03 2024 |
R-4.5-win | OK | Nov 03 2024 |
R-4.5-linux | OK | Nov 03 2024 |
R-4.4-win | OK | Nov 03 2024 |
R-4.4-mac | OK | Nov 03 2024 |
R-4.3-win | OK | Nov 03 2024 |
R-4.3-mac | OK | Nov 03 2024 |
Exports:compute_linkage_groupscompute_macrosyntenyget_syntenic_genesload_orthologsplot_chord_diagramplot_macrosyntenyplot_oxford_gridreorder_macrosyntenyreorder_multiple_macrosynteniesreverse_species_ordersubset_linkage_orthologs
Dependencies:clicolorspacecpp11dplyrfansifarvergenericsggplot2gluegtableigraphisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigplyrpurrrR6RColorBrewerRcppreshape2rlangscalesstringistringrtibbletidyrtidyselectutf8vctrsviridisLitewithr
Readme and manuals
Help Manual
Help page | Topics |
---|---|
Compute Linkage groups | compute_linkage_groups |
Compute significant macrosynteny blocks | compute_macrosynteny |
get the syntenic genes as a table | get_syntenic_genes |
load orthologs with their genomic coordinates. | load_orthologs |
plot the Macro-synteny as a chord diagram | plot_chord_diagram |
Plot Macro-synteny | plot_macrosynteny |
plot the Macro-synteny as an oxford grid. | plot_oxford_grid |
Reorder the mbh_df before plotting | reorder_macrosynteny |
Reorder the chromosomes of two or more species before plotting | reorder_multiple_macrosyntenies |
Reverse order of the species in an orthologs_df. | reverse_species_order |
Subset Orthologs contained in conserved linkage groups | subset_linkage_orthologs |