martino-vic
src/lingpy/convert/plot.py
changed.
Showing 1 of 1 files from the diff.
@@ -979,7 +979,7 @@
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| 979 | 979 | ||
| 980 | 980 | # plot the reference tree |
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| 981 | 981 | if keywords['show_tree']: |
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| 982 | - | tree_matrix, taxa = nwk2tree_matrix(tree) |
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| 982 | + | tree_matrix, taxa_in_matrix = nwk2tree_matrix(tree) |
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| 983 | 983 | ax1 = fig.add_axes( |
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| 984 | 984 | [ |
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| 985 | 985 | keywords['left'], |
@@ -991,7 +991,7 @@
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| 991 | 991 | # [0.01,0.1,0.2,0.7]) |
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| 992 | 992 | d = sch.dendrogram( |
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| 993 | 993 | np.array(tree_matrix), |
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| 994 | - | labels=[t for t in taxa], |
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| 994 | + | labels=[t for t in taxa_in_matrix], |
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| 995 | 995 | orientation='left', |
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| 996 | 996 | ||
| 997 | 997 | ) |
@@ -1007,11 +1007,18 @@
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| 1007 | 1007 | else: |
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| 1008 | 1008 | left = keywords['left'] |
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| 1009 | 1009 | taxa = tree.taxa |
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| 1010 | + | taxa_in_matrix = taxa |
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| 1010 | 1011 | ||
| 1011 | 1012 | # start iterating over taxa in order of the reference tree and fill in the |
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| 1012 | 1013 | # matrix with numbers of shared cognates |
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| 1013 | 1014 | if keywords['matrix']: |
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| 1014 | - | matrix = keywords['matrix'] |
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| 1015 | + | matrix = [[cell for cell in row] for row in keywords['matrix']] |
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| 1016 | + | conv = {} |
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| 1017 | + | for i, taxon in enumerate(taxa): |
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| 1018 | + | conv[i] = taxa_in_matrix.index(taxon) |
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| 1019 | + | for i, taxonA in enumerate(taxa): |
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| 1020 | + | for j, taxonB in enumerate(taxa): |
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| 1021 | + | matrix[i][j] = keywords["matrix"][conv[i]][conv[j]] |
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| 1015 | 1022 | else: |
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| 1016 | 1023 | for i, taxonA in enumerate(taxa): |
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| 1017 | 1024 | for j, taxonB in enumerate(taxa): |
| Files | Coverage |
|---|---|
| src/lingpy | 87.57% |
| tests | 98.86% |
| Project Totals (123 files) | 89.24% |
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