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In viewpoly: A Shiny App to Visualize Genetic Maps and QTL Analysis in Polyploid Species
VIEWpoly Citation
Taniguti, C. H., de Siqueira Gesteira, G., Lau, J., da Silva Pereira, G., Zeng, Z.-B., Byrne, D., Riera-Lizarazu, O., & Mollinari, M. (2022). VIEWpoly: a visualization tool to integrate and explore results of polyploid genetic analysis. Journal of Open Source Software, 7(74), 4242. https://doi.org/10.21105/joss.04242
Genetic Mapping Software
Please cite the appropriate genetic mapping software used:
MAPpoly
Mollinari, M., & Garcia, A. A. F. (2019). Linkage Analysis and Haplotype Phasing in Experimental Autopolyploid Populations with High Ploidy Level Using Hidden Markov Models. G3: Genes|Genomes|Genetics, 9(10), 3297–3314. https://doi.org/10.1534/g3.119.400378
polymapR
Bourke, P. M., van Geest, G., Voorrips, R. E., Jansen, J., Kranenburg, T., Shahin, A., Visser, R. G. F., Arens, P., Smulders, M. J. M., & Maliepaard, C. (2018). polymapR—linkage analysis and genetic map construction from F1 populations of outcrossing polyploids. Bioinformatics, 34(20), 3496–3502. https://doi.org/10.1093/bioinformatics/bty371
OneMap
Taniguti, C. H., Taniguti, L. M., Amadeu, R. R., Lau, J., Gesteira, G. de S., Oliveira, T. de P., Ferreira, G. C., Pereira, G. da S., Byrne, D., Mollinari, M., Riera-Lizarazu, O., & Garcia, A. A. F. (2022). Developing best practices for genotyping-by-sequencing analysis in the construction of linkage maps. GigaScience, 12. https://doi.org/10.1093/gigascience/giad092
Reporting Genetic Map Results
When publishing genetic maps visualized in VIEWmap:
Include:
1. VIEWpoly citation for visualization
2. MAPpoly, polymapR, or OneMap citation for map construction
3. Population type and size
4. Ploidy level
5. Number of markers and linkage groups
6. Total map length
7. Average marker spacing
Map Quality Metrics:
- Segregation distortion patterns
- Missing data percentage
- Largest gaps between markers
- Heat map of recombination fractions (if available)
Additional Resources
MAPpoly Tutorial: https://mmollina.github.io/MAPpoly/
polymapR Manual: https://cran.r-project.org/web/packages/polymapR/
OneMap Documentation: https://cran.r-project.org/web/packages/OneMap/
VIEWpoly Tutorial: https://cristianetaniguti.github.io/viewpoly_vignettes/
Breeding Insight: https://www.breedinginsight.org
Try the viewpoly package in your browser
Any scripts or data that you put into this service are public.
viewpoly documentation built on July 11, 2026, 1:08 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
VIEWpoly Citation
Taniguti, C. H., de Siqueira Gesteira, G., Lau, J., da Silva Pereira, G., Zeng, Z.-B., Byrne, D., Riera-Lizarazu, O., & Mollinari, M. (2022). VIEWpoly: a visualization tool to integrate and explore results of polyploid genetic analysis. Journal of Open Source Software, 7(74), 4242. https://doi.org/10.21105/joss.04242
Genetic Mapping Software
Please cite the appropriate genetic mapping software used:
MAPpoly
Mollinari, M., & Garcia, A. A. F. (2019). Linkage Analysis and Haplotype Phasing in Experimental Autopolyploid Populations with High Ploidy Level Using Hidden Markov Models. G3: Genes|Genomes|Genetics, 9(10), 3297–3314. https://doi.org/10.1534/g3.119.400378
polymapR
Bourke, P. M., van Geest, G., Voorrips, R. E., Jansen, J., Kranenburg, T., Shahin, A., Visser, R. G. F., Arens, P., Smulders, M. J. M., & Maliepaard, C. (2018). polymapR—linkage analysis and genetic map construction from F1 populations of outcrossing polyploids. Bioinformatics, 34(20), 3496–3502. https://doi.org/10.1093/bioinformatics/bty371
OneMap
Taniguti, C. H., Taniguti, L. M., Amadeu, R. R., Lau, J., Gesteira, G. de S., Oliveira, T. de P., Ferreira, G. C., Pereira, G. da S., Byrne, D., Mollinari, M., Riera-Lizarazu, O., & Garcia, A. A. F. (2022). Developing best practices for genotyping-by-sequencing analysis in the construction of linkage maps. GigaScience, 12. https://doi.org/10.1093/gigascience/giad092
Reporting Genetic Map Results
When publishing genetic maps visualized in VIEWmap:
Include: 1. VIEWpoly citation for visualization 2. MAPpoly, polymapR, or OneMap citation for map construction 3. Population type and size 4. Ploidy level 5. Number of markers and linkage groups 6. Total map length 7. Average marker spacing
Map Quality Metrics: - Segregation distortion patterns - Missing data percentage - Largest gaps between markers - Heat map of recombination fractions (if available)
Additional Resources
MAPpoly Tutorial: https://mmollina.github.io/MAPpoly/
polymapR Manual: https://cran.r-project.org/web/packages/polymapR/
OneMap Documentation: https://cran.r-project.org/web/packages/OneMap/
VIEWpoly Tutorial: https://cristianetaniguti.github.io/viewpoly_vignettes/
Breeding Insight: https://www.breedinginsight.org
Try the viewpoly package in your browser
Any scripts or data that you put into this service are public.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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