Visualization scripts for the Soybase soybean parentage data.
| Cytoscape | visNetwork |
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The main script is CytoscapePedigree.R. This script uses the soybean parentage data in the SoybasePedigreeData.csv table to make pedigree trees for a given soybean cultivar with Cytoscape. Because of this Cytoscape has to be installed for the script to work. The MakeFullGraph.R script is used to make an igraph object using the full set of pedigree data. This graph is then used in the GetPedigree_fromGraph function to rapidly build a pedigree tree for some given cultivar. This function is a faster replacement for the less efficient GetPedigree function.
After that, the easiest way to use this script would probably be to clone this repository as a new project in RStudio and run it from there. I'd also recommend using the yFiles Hierarchic layout in cytoscape to visualize the pedigrees. The other layouts have tended to look pretty confusing.
I've made a small shiny app to show these pedigree networks.
Warning
There are some things to look out for in the app. If a pedigree branch ends before the selected depth, check the page of the last node (by clicking on the link that pops up when you hover over the last node). Soybase doesn't always have complete data in the pedigree fields of their table and sometimes moves this data to the comments section of the table. Also be suspicious of branches that end in a self (see the future work section)
A shiny app that includes cytoscape would be nice so that everything can be done in the same place. The cyjShiny package looks promising, but I'll have to mess around with it.Add functions to make more traditional text based pedigrees. While not as helpful for visualizing the pedigrees (IMO), could still be helpful to augment the plots with an alternate representation of the same information.- Add tables with supplementary data for the cultivars.
I'll need to track down phenotype data, but haplotype data from soybase would also be a good place to start. Could be used to investigate patterns in phenotypic and genotypic similarity/differences. - Reformatting this repository as a R package would make use easier.
- Add a tool to the shiny app that lets a user upload a file of male/female lines and get back the pedigree for each line in a new file that they can then download.
- Add nodes/edges to connect a cultivar to its selfs (ex: Lee -> Lee (2)).