Genealogy part 8 - veeninglab/BactMAP GitHub Wiki

Resources

  1. The example dataset & more information on the data structure of genealogy data.
  2. Importing genealogy data using extr_SuperSeggerClist or extr_Oufti.
  3. Plotting trees using plotTreeBasic.
  4. The ggtree book.
  5. Using ggraph for network plots.
  6. Making interactive plots with plotly.
  7. Hadley Wickham's ggplot2 book (reference below).
  8. More on working with phylogenetic trees using ape and network data using igraph.

References

Wickham, Hadley. 2009. Ggplot2: Elegant Graphics for Data Analysis. 1st ed. Springer.

[Yu, Guangchuang, David K. Smith, Huachen Zhu, Yi Guan, and Tommy Tsan-Yuk Lam. 2017. “Ggtree: An R Package for Visualization and Annotation of Phylogenetic Trees with Their Covariates and Other Associated Data.” Methods in Ecology and Evolution 8 (1):28–36.] (https://doi.org/10.1111/2041-210X.12628)

Cass, J. A., Stylianidou, S., Kuwada, N. J., Traxler, B. and Wiggins, P. A. (2017), Probing bacterial cell biology using image cytometry. Molecular Microbiology.

Stylianidou, S., Brennan, C., Nissen, S. B., Kuwada, N. J., & Wiggins, P. A. (2016). SuperSegger: robust image segmentation, analysis and lineage tracking of bacterial cells. Molecular Microbiology, 102(4), 690-700

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