About this R Notebook

In this notebook, I am playing with the R package ggtree (https://bioconductor.org/packages/release/bioc/html/ggtree.html) and using it look at some stopwords from the R package quanteda (https://quanteda.io/index.html). I wanted to see which stopwords from Norwegian and Swedish I can recognize from Danish. So, instead of printing out the stopwords in the R Console, I made the “word trees” below.

ggtree is a package that can be used for the visualization and annotation of phylogenetic trees and it is one of many R packages in Bioconductor. Bioconductor uses R and it provides tools for the analysis and comprehension of high-throughput genomic data. More information about Biocondutor and its other packages can be found at https://www.bioconductor.org.

If you also use Python, there is another great module called ETE Toolkit for automated manipulation, analysis and visualization of phylogenetic trees. More information about ETE Toolkit can be found at http://etetoolkit.org . MEGA, a software suite for analyzing DNA and protein data from species and populations, can also be used for sequence alignment and generation of phylogenetic trees and newick file formats among other things. More information about MEGA can be found at https://megasoftware.net.

Dansk (Danish) Stopwords Tree

I was told that one of the benefits of learning Danish is that you get to learn three languages (Danish, Norwegian, and Swedish) at the same time. To me, Bokmål (one of the Norwegian written languages) is very similiar to written Danish however the Norwegian pronunciation is different. And I find that the Nowegian pronunciation is similar to Swedish pronunciation. Below are some websites in the different languages.

If you are interested in the Danish language, I have a Flexdashboard (in Danish on this RPub page) with the resources that I used while I was taking my Danish language courses.

Norsk (Norwegian) Stopwords Tree

The red words are the Norwegian words that I recognize from Danish.

Svensk (Swedish) Stopwords Tree

The red words are the Swedish words that I recognize from Danish.

References

  • library(ggtree) : Yu G, Smith D, Zhu H, Guan Y, Lam TT (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, 28-36. doi: 10.1111/2041-210X.12628, http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12628/abstract.

Yu G, Lam TT, Zhu H, Guan Y (2018). “Two methods for mapping and visualizing associated data on phylogeny using ggtree.” Molecular Biology and Evolution. doi: 10.1093/molbev/msy194, https://doi.org/10.1093/molbev/msy194.

  • library(ggtree) website : https://bioconductor.org/packages/release/bioc/html/ggtree.html

  • library(quanteda) : Benoit, Kenneth, Kohei Watanabe, Haiyan Wang, Paul Nulty, Adam Obeng, Stefan Müller, and Akitaka Matsuo. (2018) “quanteda: An R package for the quantitative analysis of textual data”. Journal of Open Source Software. 3(30), 774. https://doi.org/10.21105/joss.00774.

  • library(quanteda) website : https://quanteda.io/index.html

  • Bioconductor (tools for genomic data analysis and comprehension) : https://www.bioconductor.org

  • MEGA (software suite for analyzing DNA and protein data from species and populations) : MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Kumar S, Stecher G, Li M, Knyaz C, and Tamura K ( 2018) Molecular Biology and Evolution 35:1547-1549 (https://www.megasoftware.net/citations)

  • MEGA website: https://megasoftware.net

  • ETE Toolkit (python module for phylogenetic analysis) : ETE 3: Reconstruction, analysis and visualization of phylogenomic data. Jaime Huerta-Cepas, Francois Serra and Peer Bork. Mol Biol Evol 2016; doi: 10.1093/molbev/msw046

  • ETE Toolkit website: http://etetoolkit.org

  • ggplot2 elegant graphics for data analysis by Hadley Wickham