lingpy / lingpy
Showing 1 of 1 files from the diff.

@@ -979,7 +979,7 @@
 979 979 980 980 ` # plot the reference tree` 981 981 ` if keywords['show_tree']:` 982 - ` tree_matrix, taxa = nwk2tree_matrix(tree)` 982 + ` tree_matrix, taxa_in_matrix = nwk2tree_matrix(tree)` 983 983 ` ax1 = fig.add_axes(` 984 984 ` [` 985 985 ` keywords['left'],`
@@ -991,7 +991,7 @@
 991 991 ` # [0.01,0.1,0.2,0.7])` 992 992 ` d = sch.dendrogram(` 993 993 ` np.array(tree_matrix),` 994 - ` labels=[t for t in taxa],` 994 + ` labels=[t for t in taxa_in_matrix],` 995 995 ` orientation='left',` 996 996 997 997 ` )`
@@ -1007,11 +1007,18 @@
 1007 1007 ` else:` 1008 1008 ` left = keywords['left']` 1009 1009 ` taxa = tree.taxa` 1010 + ` taxa_in_matrix = taxa` 1010 1011 1011 1012 ` # start iterating over taxa in order of the reference tree and fill in the` 1012 1013 ` # matrix with numbers of shared cognates` 1013 1014 ` if keywords['matrix']:` 1014 - ` matrix = keywords['matrix']` 1015 + ` matrix = [[cell for cell in row] for row in keywords['matrix']]` 1016 + ` conv = {}` 1017 + ` for i, taxon in enumerate(taxa):` 1018 + ` conv[i] = taxa_in_matrix.index(taxon)` 1019 + ` for i, taxonA in enumerate(taxa):` 1020 + ` for j, taxonB in enumerate(taxa):` 1021 + ` matrix[i][j] = keywords["matrix"][conv[i]][conv[j]]` 1015 1022 ` else:` 1016 1023 ` for i, taxonA in enumerate(taxa):` 1017 1024 ` for j, taxonB in enumerate(taxa):`
Files Coverage
src/lingpy 87.57%
tests 98.86%
Project Totals (123 files) 89.24%

#### No yaml found.

Create your codecov.yml to customize your Codecov experience

Sunburst
The inner-most circle is the entire project, moving away from the center are folders then, finally, a single file. The size and color of each slice is representing the number of statements and the coverage, respectively.
Icicle
The top section represents the entire project. Proceeding with folders and finally individual files. The size and color of each slice is representing the number of statements and the coverage, respectively.
Grid
Each block represents a single file in the project. The size and color of each block is represented by the number of statements and the coverage, respectively.