Overview : | Step-by-step tutorial : | 1 - Pre-processing : | 1.1 - Foreword : | 1.2 - Example using two species (rbhXpress) : | 1.3 - Example using 3 species (Orthofinder) : | 2 - Load the data : | 3 - Compute linkage groups : | 4 - Reorder chromosome levels to group the linkage groups in clusters : | 4.1 - Automatic reordering using a network-based greedy algorithm : | 4.2 - Manually reorder/subset the Chromosomes : | 5 - Plot directly with reordering the linkage groups and coloring : | 6 - Customize the plots : | 6.1 - customize the legend : | 6.2 - change the color palette : | 7 - Integrate additional information using colors : | 8 - plot a chord diagram :
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-4.7-any)macrosyntR_0.3.4.zip(r-4.6-any)macrosyntR_0.3.4.zip(r-4.5-any)
macrosyntR_0.3.4.tgz(r-4.6-any)macrosyntR_0.3.4.tgz(r-4.5-any)
macrosyntR_0.3.4.tar.gz(r-4.7-any)macrosyntR_0.3.4.tar.gz(r-4.6-any)
macrosyntR_0.3.4.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
macrosyntR/json (API)
| # 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 from:a86189db19. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | OK | 158 | ||
| source / vignettes | OK | 253 | ||
| linux-release | OK | 154 | ||
| macos-release | OK | 183 | ||
| macos-oldrel | OK | 205 | ||
| windows-devel | OK | 96 | ||
| windows-release | OK | 139 | ||
| windows-oldrel | OK | 103 | ||
| wasm-release | OK | 127 |
Exports:compute_linkage_groupscompute_macrosyntenyget_syntenic_genesload_orthologsplot_chord_diagramplot_macrosyntenyplot_oxford_gridreorder_macrosyntenyreorder_multiple_macrosynteniesreverse_species_ordersubset_linkage_orthologs
Dependencies:clicpp11dplyrfarvergenericsggplot2gluegtableigraphisobandlabelinglatticelifecyclemagrittrMatrixpillarpkgconfigplyrpurrrR6RColorBrewerRcppreshape2rlangS7scalesstringistringrtibbletidyrtidyselectutf8vctrsviridisLitewithr
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 |