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### bulk module - fix the duplicates_index mapping of `Matrix_ID_mapping` - fix the hub genes plot of `pyWGCNA.plot_sub_network` - fix the backupgene of `pyGSEA.geneset_enrichment` to support the rare species - add the module matrix plot in `pyWGCNA.plot_matrix` ### single module - add the `rank_genes_groups` check in `pySCSA` ### bulk2single module - fix the import error of `deepforest`
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| # Details | ||
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| Date : 2023-05-06 17:08:26 | ||
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| Directory : ./Pyomic | ||
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| Total : 100 files, 21262 codes, 7774 comments, 5304 blanks, all 34340 lines, 26.77% comment rate | ||
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| [summary](results.md) | ||
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| ## Files | ||
| | filename | language | code | comment | blank | total | comment rate | | ||
| | :--- | :--- | ---: | ---: | ---: | ---: | ---: | | ||
| | [__init__.py](../Pyomic/__init__.py) | Python | 9 | 2 | 6 | 17 | 18.18% | | ||
| | [bulk/_Deseq2.py](../Pyomic/bulk/_Deseq2.py) | Python | 231 | 148 | 41 | 420 | 39.05% | | ||
| | [bulk/_Enrichment.py](../Pyomic/bulk/_Enrichment.py) | Python | 105 | 239 | 17 | 361 | 69.48% | | ||
| | [bulk/_Gene_module.py](../Pyomic/bulk/_Gene_module.py) | Python | 537 | 108 | 96 | 741 | 16.74% | | ||
| | [bulk/__init__.py](../Pyomic/bulk/__init__.py) | Python | 7 | 4 | 2 | 13 | 36.36% | | ||
| | [bulk/_chm13.py](../Pyomic/bulk/_chm13.py) | Python | 31 | 0 | 6 | 37 | 0.00% | | ||
| | [bulk/_df_apply.py](../Pyomic/bulk/_df_apply.py) | Python | 32 | 15 | 15 | 62 | 31.91% | | ||
| | [bulk/_dynamicTree.py](../Pyomic/bulk/_dynamicTree.py) | Python | 658 | 75 | 187 | 920 | 10.23% | | ||
| | [bulk/_network.py](../Pyomic/bulk/_network.py) | Python | 125 | 49 | 22 | 196 | 28.16% | | ||
| | [bulk/_tcga.py](../Pyomic/bulk/_tcga.py) | Python | 196 | 65 | 36 | 297 | 24.90% | | ||
| | [bulk2single/__init__.py](../Pyomic/bulk2single/__init__.py) | Python | 4 | 2 | 1 | 7 | 33.33% | | ||
| | [bulk2single/_bulk2single.py](../Pyomic/bulk2single/_bulk2single.py) | Python | 152 | 76 | 20 | 248 | 33.33% | | ||
| | [bulk2single/_map_utils.py](../Pyomic/bulk2single/_map_utils.py) | Python | 554 | 61 | 145 | 760 | 9.92% | | ||
| | [bulk2single/_map_utils1.py](../Pyomic/bulk2single/_map_utils1.py) | Python | 478 | 38 | 122 | 638 | 7.36% | | ||
| | [bulk2single/_single2spatial.py](../Pyomic/bulk2single/_single2spatial.py) | Python | 168 | 67 | 27 | 262 | 28.51% | | ||
| | [bulk2single/_utils.py](../Pyomic/bulk2single/_utils.py) | Python | 155 | 51 | 39 | 245 | 24.76% | | ||
| | [bulk2single/_vae.py](../Pyomic/bulk2single/_vae.py) | Python | 187 | 2 | 51 | 240 | 1.06% | | ||
| | [mofapy2/__init__.py](../Pyomic/mofapy2/__init__.py) | Python | 2 | 0 | 1 | 3 | 0.00% | | ||
| | [mofapy2/build_model/__init__.py](../Pyomic/mofapy2/build_model/__init__.py) | Python | 0 | 0 | 1 | 1 | 0.00% | | ||
| | [mofapy2/build_model/build_model.py](../Pyomic/mofapy2/build_model/build_model.py) | Python | 202 | 84 | 71 | 357 | 29.37% | | ||
| | [mofapy2/build_model/init_model.py](../Pyomic/mofapy2/build_model/init_model.py) | Python | 348 | 251 | 139 | 738 | 41.90% | | ||
| | [mofapy2/build_model/save_model.py](../Pyomic/mofapy2/build_model/save_model.py) | Python | 296 | 132 | 120 | 548 | 30.84% | | ||
| | [mofapy2/build_model/train_model.py](../Pyomic/mofapy2/build_model/train_model.py) | Python | 17 | 7 | 11 | 35 | 29.17% | | ||
| | [mofapy2/build_model/utils.py](../Pyomic/mofapy2/build_model/utils.py) | Python | 62 | 22 | 25 | 109 | 26.19% | | ||
| | [mofapy2/config.py](../Pyomic/mofapy2/config.py) | Python | 12 | 6 | 4 | 22 | 33.33% | | ||
| | [mofapy2/core/BayesNet.py](../Pyomic/mofapy2/core/BayesNet.py) | Python | 344 | 140 | 117 | 601 | 28.93% | | ||
| | [mofapy2/core/__init__.py](../Pyomic/mofapy2/core/__init__.py) | Python | 1 | 0 | 1 | 2 | 0.00% | | ||
| | [mofapy2/core/distributions/__init__.py](../Pyomic/mofapy2/core/distributions/__init__.py) | Python | 9 | 1 | 0 | 10 | 10.00% | | ||
| | [mofapy2/core/distributions/basic_distributions.py](../Pyomic/mofapy2/core/distributions/basic_distributions.py) | Python | 39 | 51 | 14 | 104 | 56.67% | | ||
| | [mofapy2/core/distributions/bernoulli.py](../Pyomic/mofapy2/core/distributions/bernoulli.py) | Python | 26 | 10 | 12 | 48 | 27.78% | | ||
| | [mofapy2/core/distributions/bernoulli_gaussian.py](../Pyomic/mofapy2/core/distributions/bernoulli_gaussian.py) | Python | 57 | 39 | 18 | 114 | 40.63% | | ||
| | [mofapy2/core/distributions/beta.py](../Pyomic/mofapy2/core/distributions/beta.py) | Python | 32 | 14 | 8 | 54 | 30.43% | | ||
| | [mofapy2/core/distributions/binomial.py](../Pyomic/mofapy2/core/distributions/binomial.py) | Python | 31 | 14 | 10 | 55 | 31.11% | | ||
| | [mofapy2/core/distributions/gamma.py](../Pyomic/mofapy2/core/distributions/gamma.py) | Python | 33 | 15 | 12 | 60 | 31.25% | | ||
| | [mofapy2/core/distributions/multi_task_GP.py](../Pyomic/mofapy2/core/distributions/multi_task_GP.py) | Python | 0 | 783 | 0 | 783 | 100.00% | | ||
| | [mofapy2/core/distributions/multivariate_gaussian.py](../Pyomic/mofapy2/core/distributions/multivariate_gaussian.py) | Python | 195 | 82 | 47 | 324 | 29.60% | | ||
| | [mofapy2/core/distributions/poisson.py](../Pyomic/mofapy2/core/distributions/poisson.py) | Python | 30 | 14 | 10 | 54 | 31.82% | | ||
| | [mofapy2/core/distributions/univariate_gaussian.py](../Pyomic/mofapy2/core/distributions/univariate_gaussian.py) | Python | 34 | 19 | 13 | 66 | 35.85% | | ||
| | [mofapy2/core/gp_utils.py](../Pyomic/mofapy2/core/gp_utils.py) | Python | 59 | 70 | 22 | 151 | 54.26% | | ||
| | [mofapy2/core/gpu_utils.py](../Pyomic/mofapy2/core/gpu_utils.py) | Python | 52 | 15 | 13 | 80 | 22.39% | | ||
| | [mofapy2/core/nodes/Alpha_nodes.py](../Pyomic/mofapy2/core/nodes/Alpha_nodes.py) | Python | 102 | 35 | 43 | 180 | 25.55% | | ||
| | [mofapy2/core/nodes/Kc_node.py](../Pyomic/mofapy2/core/nodes/Kc_node.py) | Python | 55 | 37 | 28 | 120 | 40.22% | | ||
| | [mofapy2/core/nodes/Kg_node.py](../Pyomic/mofapy2/core/nodes/Kg_node.py) | Python | 50 | 31 | 20 | 101 | 38.27% | | ||
| | [mofapy2/core/nodes/Sigma_node.py](../Pyomic/mofapy2/core/nodes/Sigma_node.py) | Python | 478 | 424 | 129 | 1,031 | 47.01% | | ||
| | [mofapy2/core/nodes/Tau_nodes.py](../Pyomic/mofapy2/core/nodes/Tau_nodes.py) | Python | 86 | 31 | 36 | 153 | 26.50% | | ||
| | [mofapy2/core/nodes/Theta_nodes.py](../Pyomic/mofapy2/core/nodes/Theta_nodes.py) | Python | 107 | 36 | 47 | 190 | 25.17% | | ||
| | [mofapy2/core/nodes/U_nodes.py](../Pyomic/mofapy2/core/nodes/U_nodes.py) | Python | 112 | 33 | 45 | 190 | 22.76% | | ||
| | [mofapy2/core/nodes/W_nodes.py](../Pyomic/mofapy2/core/nodes/W_nodes.py) | Python | 146 | 48 | 64 | 258 | 24.74% | | ||
| | [mofapy2/core/nodes/Y_nodes.py](../Pyomic/mofapy2/core/nodes/Y_nodes.py) | Python | 72 | 14 | 22 | 108 | 16.28% | | ||
| | [mofapy2/core/nodes/Z_nodes.py](../Pyomic/mofapy2/core/nodes/Z_nodes.py) | Python | 235 | 72 | 74 | 381 | 23.45% | | ||
| | [mofapy2/core/nodes/Z_nodes_GP.py](../Pyomic/mofapy2/core/nodes/Z_nodes_GP.py) | Python | 155 | 21 | 45 | 221 | 11.93% | | ||
| | [mofapy2/core/nodes/Z_nodes_GP_mv.py](../Pyomic/mofapy2/core/nodes/Z_nodes_GP_mv.py) | Python | 120 | 40 | 42 | 202 | 25.00% | | ||
| | [mofapy2/core/nodes/ZgU_node.py](../Pyomic/mofapy2/core/nodes/ZgU_node.py) | Python | 117 | 25 | 38 | 180 | 17.61% | | ||
| | [mofapy2/core/nodes/__init__.py](../Pyomic/mofapy2/core/nodes/__init__.py) | Python | 17 | 0 | 0 | 17 | 0.00% | | ||
| | [mofapy2/core/nodes/basic_nodes.py](../Pyomic/mofapy2/core/nodes/basic_nodes.py) | Python | 64 | 37 | 23 | 124 | 36.63% | | ||
| | [mofapy2/core/nodes/multiview_nodes.py](../Pyomic/mofapy2/core/nodes/multiview_nodes.py) | Python | 69 | 72 | 26 | 167 | 51.06% | | ||
| | [mofapy2/core/nodes/nongaussian_nodes.py](../Pyomic/mofapy2/core/nodes/nongaussian_nodes.py) | Python | 269 | 179 | 110 | 558 | 39.96% | | ||
| | [mofapy2/core/nodes/variational_nodes.py](../Pyomic/mofapy2/core/nodes/variational_nodes.py) | Python | 96 | 125 | 39 | 260 | 56.56% | | ||
| | [mofapy2/core/utils.py](../Pyomic/mofapy2/core/utils.py) | Python | 64 | 51 | 21 | 136 | 44.35% | | ||
| | [mofapy2/run/__init__.py](../Pyomic/mofapy2/run/__init__.py) | Python | 0 | 0 | 1 | 1 | 0.00% | | ||
| | [mofapy2/run/entry_point.py](../Pyomic/mofapy2/run/entry_point.py) | Python | 838 | 322 | 234 | 1,394 | 27.76% | | ||
| | [mofapy2/simulate/__init__.py](../Pyomic/mofapy2/simulate/__init__.py) | Python | 0 | 0 | 1 | 1 | 0.00% | | ||
| | [mofapy2/simulate/simulate_mofa.py](../Pyomic/mofapy2/simulate/simulate_mofa.py) | Python | 113 | 36 | 23 | 172 | 24.16% | | ||
| | [mofapy2/version.py](../Pyomic/mofapy2/version.py) | Python | 1 | 0 | 1 | 2 | 0.00% | | ||
| | [nocd/__init__.py](../Pyomic/nocd/__init__.py) | Python | 6 | 0 | 1 | 7 | 0.00% | | ||
| | [nocd/data.py](../Pyomic/nocd/data.py) | Python | 39 | 19 | 12 | 70 | 32.76% | | ||
| | [nocd/generate.py](../Pyomic/nocd/generate.py) | Python | 24 | 21 | 5 | 50 | 46.67% | | ||
| | [nocd/metrics/__init__.py](../Pyomic/nocd/metrics/__init__.py) | Python | 2 | 0 | 1 | 3 | 0.00% | | ||
| | [nocd/metrics/supervised.py](../Pyomic/nocd/metrics/supervised.py) | Python | 68 | 48 | 13 | 129 | 41.38% | | ||
| | [nocd/metrics/unsupervised.py](../Pyomic/nocd/metrics/unsupervised.py) | Python | 53 | 36 | 15 | 104 | 40.45% | | ||
| | [nocd/nn/__init__.py](../Pyomic/nocd/nn/__init__.py) | Python | 3 | 0 | 1 | 4 | 0.00% | | ||
| | [nocd/nn/decoder.py](../Pyomic/nocd/nn/decoder.py) | Python | 64 | 48 | 18 | 130 | 42.86% | | ||
| | [nocd/nn/gcn.py](../Pyomic/nocd/nn/gcn.py) | Python | 71 | 16 | 15 | 102 | 18.39% | | ||
| | [nocd/nn/imrpoved_gcn.py](../Pyomic/nocd/nn/imrpoved_gcn.py) | Python | 68 | 19 | 13 | 100 | 21.84% | | ||
| | [nocd/sampler.py](../Pyomic/nocd/sampler.py) | Python | 32 | 8 | 8 | 48 | 20.00% | | ||
| | [nocd/train.py](../Pyomic/nocd/train.py) | Python | 74 | 56 | 26 | 156 | 43.08% | | ||
| | [nocd/utils.py](../Pyomic/nocd/utils.py) | Python | 82 | 41 | 20 | 143 | 33.33% | | ||
| | [single/README.md](../Pyomic/single/README.md) | Markdown | 151 | 0 | 12 | 163 | 0.00% | | ||
| | [single/_SCSA.py](../Pyomic/single/_SCSA.py) | Python | 964 | 199 | 125 | 1,288 | 17.11% | | ||
| | [single/__init__.py](../Pyomic/single/__init__.py) | Python | 9 | 2 | 1 | 12 | 18.18% | | ||
| | [single/_anno.py](../Pyomic/single/_anno.py) | Python | 268 | 157 | 37 | 462 | 36.94% | | ||
| | [single/_aucell.py](../Pyomic/single/_aucell.py) | Python | 123 | 81 | 20 | 224 | 39.71% | | ||
| | [single/_cosg.py](../Pyomic/single/_cosg.py) | Python | 379 | 108 | 103 | 590 | 22.18% | | ||
| | [single/_cpdb.py](../Pyomic/single/_cpdb.py) | Python | 137 | 164 | 25 | 326 | 54.49% | | ||
| | [single/_mofa.py](../Pyomic/single/_mofa.py) | Python | 102 | 118 | 13 | 233 | 53.64% | | ||
| | [single/_nocd.py](../Pyomic/single/_nocd.py) | Python | 174 | 6 | 42 | 222 | 3.33% | | ||
| | [single/_scdrug.py](../Pyomic/single/_scdrug.py) | Python | 261 | 120 | 33 | 414 | 31.50% | | ||
| | [single/_scgsea.py](../Pyomic/single/_scgsea.py) | Python | 138 | 133 | 25 | 296 | 49.08% | | ||
| | [single/_via.py](../Pyomic/single/_via.py) | Python | 850 | 286 | 183 | 1,319 | 25.18% | | ||
| | [utils/__init__.py](../Pyomic/utils/__init__.py) | Python | 3 | 3 | 1 | 7 | 50.00% | | ||
| | [utils/_data.py](../Pyomic/utils/_data.py) | Python | 119 | 50 | 24 | 193 | 29.59% | | ||
| | [utils/_plot.py](../Pyomic/utils/_plot.py) | Python | 167 | 94 | 27 | 288 | 36.02% | | ||
| | [via/.idea/VIA.iml](../Pyomic/via/.idea/VIA.iml) | XML | 12 | 0 | 0 | 12 | 0.00% | | ||
| | [via/__init__.py](../Pyomic/via/__init__.py) | Python | 6 | 0 | 2 | 8 | 0.00% | | ||
| | [via/core.py](../Pyomic/via/core.py) | Python | 2,246 | 378 | 541 | 3,165 | 14.41% | | ||
| | [via/datasets_via.py](../Pyomic/via/datasets_via.py) | Python | 135 | 86 | 46 | 267 | 38.91% | | ||
| | [via/examples.py](../Pyomic/via/examples.py) | Python | 2,239 | 430 | 543 | 3,212 | 16.11% | | ||
| | [via/plotting_via.py](../Pyomic/via/plotting_via.py) | Python | 2,127 | 204 | 417 | 2,748 | 8.75% | | ||
| | [via/utils_via.py](../Pyomic/via/utils_via.py) | Python | 1,053 | 340 | 282 | 1,675 | 24.41% | | ||
| | [via/windmap.py](../Pyomic/via/windmap.py) | Python | 137 | 63 | 40 | 240 | 31.50% | | ||
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| [summary](results.md) |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
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| Original file line number | Diff line number | Diff line change |
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| # Summary | ||
|
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| Date : 2023-05-06 17:08:26 | ||
|
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| Directory : ./Pyomic | ||
|
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||
| Total : 100 files, 21262 codes, 7774 comments, 5304 blanks, all 34340 lines, 26.77% comment rate | ||
|
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| [details](details.md) | ||
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| ## Languages | ||
| | language | files | code | comment | blank | total | comment rate | | ||
| | :--- | ---: | ---: | ---: | ---: | ---: | ---: | | ||
| | Python | 98 | 21,099 | 7,774 | 5,292 | 34,165 | 26.92% | | ||
| | Markdown | 1 | 151 | 0 | 12 | 163 | 0.00% | | ||
| | XML | 1 | 12 | 0 | 0 | 12 | 0.00% | | ||
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| ## Directories | ||
| | path | files | code | comment | blank | total | comment rate | | ||
| | :--- | ---: | ---: | ---: | ---: | ---: | ---: | | ||
| | . | 100 | 21,262 | 7,774 | 5,304 | 34,340 | 26.77% | | ||
| | bulk | 9 | 1,922 | 703 | 422 | 3,047 | 26.78% | | ||
| | bulk2single | 7 | 1,698 | 297 | 405 | 2,400 | 14.89% | | ||
| | mofapy2 | 47 | 5,247 | 3,438 | 1,781 | 10,466 | 39.59% | | ||
| | mofapy2/build_model | 6 | 925 | 496 | 367 | 1,788 | 34.90% | | ||
| | mofapy2/core | 34 | 3,356 | 2,578 | 1,149 | 7,083 | 43.44% | | ||
| | mofapy2/core/distributions | 11 | 486 | 1,042 | 144 | 1,672 | 68.19% | | ||
| | mofapy2/core/nodes | 18 | 2,350 | 1,260 | 831 | 4,441 | 34.90% | | ||
| | mofapy2/run | 2 | 838 | 322 | 235 | 1,395 | 27.76% | | ||
| | mofapy2/simulate | 2 | 113 | 36 | 24 | 173 | 24.16% | | ||
| | nocd | 13 | 586 | 312 | 148 | 1,046 | 34.74% | | ||
| | nocd/metrics | 3 | 123 | 84 | 29 | 236 | 40.58% | | ||
| | nocd/nn | 4 | 206 | 83 | 47 | 336 | 28.72% | | ||
| | single | 12 | 3,556 | 1,374 | 619 | 5,549 | 27.87% | | ||
| | utils | 3 | 289 | 147 | 52 | 488 | 33.72% | | ||
| | via | 8 | 7,955 | 1,501 | 1,871 | 11,327 | 15.87% | | ||
| | via/.idea | 1 | 12 | 0 | 0 | 12 | 0.00% | | ||
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| [details](details.md) |
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