diff --git a/_episodes/03-horizontalGeneTransfer-TDA.md b/_episodes/03-horizontalGeneTransfer-TDA.md index f243cad..779f452 100644 --- a/_episodes/03-horizontalGeneTransfer-TDA.md +++ b/_episodes/03-horizontalGeneTransfer-TDA.md @@ -34,20 +34,23 @@ HGT is crucial in the rapid spread of antibiotic-resistant genes among bacteria, ## Understanding Persistent Homology in the Context of HGT: Topological data analysis (TDA), in particular persistent homology, allows for identifying complex patterns and structures in large genomic datasets, -facilitating the detection of HGT of antibiotic resistance genes. - -Hierarchical data does not have holes in higger dimensions when represented +facilitating the detection of HGT of antibiotic resistance genes. Hierarchical +data does not have holes in higger dimensions when represented with a Vietoris Rips complex. A population not experiencing horizontal gene transfer and where no mutations are allowed in the same site show non-empty homology only at $ \H_0 $. Remember, $ \H_0 $ in the barcode diagram indicates the presence of connected components. +Here we will study three study cases, 1) we will show persistent homology in +vertical inheritance, 2) we will study a simulation of Horizontal Gene Transfer, +and 3), we will study the persistent homology of the resistant genes +from *Streptococcus agalactiae* that we obtained in the episode [Annotating Genomic Data](https://carpentries-incubator.github.io/pangenomics/03-annotation-with-Prokka/index.html), from the lesson [Pangenome Analysis in Prokaryotes](https://carpentries-incubator.github.io/pangenomics/index.html). In all three cases, we are going to need first +to import some libraries, then to define functions, and finally to call them to visualize the data. + > ## Know more: TDA in genomics -> To learn more about applications of TDA in genomics consult the Rabadan book [Topological Data Analysis for Genomics](https://www.amazon.com.mx/Topological-Data-Analysis-Genomics-Evolution/dp/1107159547) +> To learn more about applications of TDA in genomics, consult the Rabadan book [Topological Data Analysis for Genomics](https://www.amazon.com.mx/Topological-Data-Analysis-Genomics-Evolution/dp/1107159547) {: .callout} -Here we will study three study cases, first, we will show persistent homology in vertical inheritance, then we will study a simulation of Horizontal Gene Transfer, and finally, we will study the persistent homology of the resistant genes from *Streptococcus agalactiae* that we obtained in the episode [Annotating Genomic Data](https://carpentries-incubator.github.io/pangenomics/03-annotation-with-Prokka/index.html), from the lesson [Pangenome Analysis in Prokaryotes](https://carpentries-incubator.github.io/pangenomics/index.html). - -### **Library** +### Library To begin, we will import the necessary packages. ~~~ import numpy as np