diff --git a/_episodes/03-horizontalGeneTransfer-TDA.md b/_episodes/03-horizontalGeneTransfer-TDA.md index 73291b7..d68a363 100644 --- a/_episodes/03-horizontalGeneTransfer-TDA.md +++ b/_episodes/03-horizontalGeneTransfer-TDA.md @@ -451,20 +451,38 @@ strains_names > ## Exercise 3: > Apply persistent homology and plot the persistence diagram and barcode, -> The geometric representation of the simplicial complex for various levels of filtration. +> +> Bacode population with hgt +> +> Which one is the correct answer? +> +> A) +> ~~~ +> gd.plot_persistence_barcode(persistence3) +> ~~~ +> {: .language-python} +> B) +> ~~~ +> gd.plot_persistence_diagram(persistence3, legend=True) +> ~~~ +> {: .language-python} +> +> C) > ~~~ > gd.plot_persistence_barcode(persistence3, legend=True) > ~~~ > {: .language-python} -> -> Bacode population with hgt -> ->> ->> something +>> C) +>> ~~~ +>> gd.plot_persistence_barcode(persistence3, legend=True) +>> ~~~ +>> {: .language-python} > {: .solution} {: .challenge} -> ## Exercise 4: Are the _S_agalaciae_ resistome product of vertical inheritance +> ## Exercise 4: Are the _S_agalaciae_ resistome product of vertical inheritance? +> Based on visualization of the simplicial complex at time 270. +> Which evolutionary processes may be involved in _S. agalactiae_ resistome? > ~~~ > visualize_simplicial_complex(simplex_tree3,270,strains_names) > ~~~ @@ -474,17 +492,11 @@ strains_names > Bacode population with hgt > >> ->> There is a 1-holes in the barcode diagram, so there is preliminary evidence, that this resistome was not aquired only vy vertical inheritance +>> There is a 1-holes in the barcode diagram, so there is preliminary evidence that this resistome was not acquired only vy vertical inheritance >> . > {: .solution} {: .challenge} -> ## Exercise 4: -> ->> ->> something -> {: .solution} -{: .challenge} By employing TDA and persistent homology, we gain a powerful lens through which to observe and understand the impact of HGT on bacterial genomes.