diff --git a/_episodes/03-horizontalGeneTransfer-TDA.md b/_episodes/03-horizontalGeneTransfer-TDA.md index d68a363..68f9074 100644 --- a/_episodes/03-horizontalGeneTransfer-TDA.md +++ b/_episodes/03-horizontalGeneTransfer-TDA.md @@ -419,10 +419,9 @@ strains_names ~~~ {: .output} -> ## Exercise 2: -> Apply persistent homology and plot the persistence diagram and barcode, -> Fill in the blanks -> hamming_matrix_3, values, calculate_hamming_matrix, create_complex, +> ## Exercise 2: Persistent homology of _S. agalactiae_ resistome +> Fill in the blanks with the following parameters to calculate the persisten homology of the _S. agalactiae_ resistome +> hamming_matrix_3, values, calculate_hamming_matrix, create_complex > > ~~~ > hamming_matrix_3 = __________(_____) @@ -449,8 +448,8 @@ strains_names > {: .solution} {: .challenge} -> ## Exercise 3: -> Apply persistent homology and plot the persistence diagram and barcode, +> ## Exercise 3: Plot the persistent barcode of _S. agalactiae_ resistome +> PChose the right parameters to plot the persistence diagram of _S. agalactiae_ resistome > > Bacode population with hgt > @@ -472,6 +471,7 @@ strains_names > gd.plot_persistence_barcode(persistence3, legend=True) > ~~~ > {: .language-python} +> > ## Solution >> C) >> ~~~ >> gd.plot_persistence_barcode(persistence3, legend=True) @@ -491,6 +491,7 @@ strains_names > > Bacode population with hgt > +> > ## Solution >> >> There is a 1-holes in the barcode diagram, so there is preliminary evidence that this resistome was not acquired only vy vertical inheritance >> .