144
+
+ Source code in src/pheval/analyse/analysis.py
+ 144
145
146
147
@@ -1705,7 +1776,7 @@ benchmark_generator= DiseaseBenchmarkRunOutputGenerator (),
)
+
- src.pheval.analyse.benchmark_generator
+ benchmark_generator
@@ -1235,7 +1235,7 @@
- src.pheval.analyse.benchmark_generator
+ benchmark_generator
@@ -1293,6 +1293,7 @@ Benchmark generator
+
@@ -1312,7 +1313,7 @@
Benchmark generator
- BenchmarkRunOutputGenerator
+ BenchmarkRunOutputGenerator
@@ -1327,6 +1328,8 @@ Base class for recording data required for generating benchmarking outputs.
+
+
Attributes:
@@ -1338,42 +1341,57 @@
- prioritisation_type_file_prefixprioritisation_type_file_prefix
str
- Prefix for the prioritisation type output file.
+
+
Prefix for the prioritisation type output file.
+
- y_labely_label
str
- Label for the y-axis in benchmarking outputs.
+
+
Label for the y-axis in benchmarking outputs.
+
- generate_benchmark_run_resultsgenerate_benchmark_run_results
Callable
- Callable to generate benchmark run results.
+
+
+
Callable to generate benchmark run results.
Takes parameters: input and results directory, score order, threshold, rank comparison,
-and returns BenchmarkRunResults.
+and returns BenchmarkRunResults.
+
+
- stats_comparison_file_suffixstats_comparison_file_suffix
str
- Suffix for the rank comparison file.
+
+
Suffix for the rank comparison file.
+
-
-
- Source code in src/pheval/analyse/benchmark_generator.py
- 20
+
+ Source code in src/pheval/analyse/benchmark_generator.py
+ 20
21
22
23
@@ -1411,7 +1429,7 @@ ]
stats_comparison_file_suffix : str
+
@@ -1431,6 +1449,7 @@
+
@@ -1438,7 +1457,7 @@
- DiseaseBenchmarkRunOutputGenerator
+ DiseaseBenchmarkRunOutputGenerator
@@ -1449,8 +1468,8 @@
-
- Bases: BenchmarkRunOutputGenerator
+
+ Bases: BenchmarkRunOutputGenerator
Subclass of BenchmarkRunOutputGenerator specialised
@@ -1458,6 +1477,8 @@
- prioritisation_type_file_prefixprioritisation_type_file_prefix
str
- Prefix for the disease prioritisation type file.
-Defaults to DISEASE_PLOT_FILE_PREFIX.
+
+
Prefix for the disease prioritisation type file.
+Defaults to DISEASE_PLOT_FILE_PREFIX.
+
- y_labely_label
str
- Label for the y-axis in disease prioritisation benchmarking outputs.
-Defaults to DISEASE_PLOT_Y_LABEL.
+
+
Label for the y-axis in disease prioritisation benchmarking outputs.
+Defaults to DISEASE_PLOT_Y_LABEL.
+
- generate_benchmark_run_resultsgenerate_benchmark_run_results
Callable
- Callable to generate disease prioritisation
+
+
+
Callable to generate disease prioritisation
benchmark run results. Defaults to benchmark_disease_prioritisation.
Takes parameters: input and results directory, score order, threshold, rank comparison,
-and returns BenchmarkRunResults.
+and returns BenchmarkRunResults.
+
+
- stats_comparison_file_suffixstats_comparison_file_suffix
str
- Suffix for the disease rank comparison file.
-Defaults to "-disease_summary.tsv".
+
+
Suffix for the disease rank comparison file.
+Defaults to "-disease_summary.tsv".
+
-
-
- Source code in src/pheval/analyse/benchmark_generator.py
- 102
+
+ Source code in src/pheval/analyse/benchmark_generator.py
+ 102
103
104
105
@@ -1564,7 +1600,7 @@ ] = benchmark_disease_prioritisation
stats_comparison_file_suffix : str = "-disease_summary.tsv"
+
@@ -1584,6 +1620,7 @@
@@ -1591,7 +1628,7 @@
- GeneBenchmarkRunOutputGenerator
+ GeneBenchmarkRunOutputGenerator
@@ -1602,8 +1639,8 @@
-
- Bases: BenchmarkRunOutputGenerator
+
+ Bases: BenchmarkRunOutputGenerator
Subclass of BenchmarkRunOutputGenerator specialised
@@ -1611,6 +1648,8 @@
This subclass inherits from BenchmarkRunOutputGenerator and specialises its attributes
specifically for gene prioritisation benchmarking.
+
+
Attributes:
@@ -1622,46 +1661,61 @@
- prioritisation_type_file_prefixprioritisation_type_file_prefix
str
- Prefix for the gene prioritisation type file.
-Defaults to GENE_PLOT_FILE_PREFIX.
+
+
Prefix for the gene prioritisation type file.
+Defaults to GENE_PLOT_FILE_PREFIX.
+
- y_labely_label
str
- Label for the y-axis in gene prioritisation benchmarking outputs.
-Defaults to GENE_PLOT_Y_LABEL.
+
+
Label for the y-axis in gene prioritisation benchmarking outputs.
+Defaults to GENE_PLOT_Y_LABEL.
+
- generate_benchmark_run_resultsgenerate_benchmark_run_results
Callable
- Callable to generate gene prioritisation
+
+
+
Callable to generate gene prioritisation
benchmark run results. Defaults to benchmark_gene_prioritisation.
Takes parameters: input and results directory, score order, threshold, rank comparison,
-and returns BenchmarkRunResults.
+and returns BenchmarkRunResults.
+
+
- stats_comparison_file_suffixstats_comparison_file_suffix
str
- Suffix for the gene rank comparison file.
-Defaults to "-gene_summary.tsv".
+
+
Suffix for the gene rank comparison file.
+Defaults to "-gene_summary.tsv".
+
-
-
- Source code in src/pheval/analyse/benchmark_generator.py
- 41
+
+ Source code in src/pheval/analyse/benchmark_generator.py
+ 41
42
43
44
@@ -1717,7 +1771,7 @@ ] = benchmark_gene_prioritisation
stats_comparison_file_suffix : str = "-gene_summary.tsv"
+
@@ -1737,6 +1791,7 @@
+
@@ -1744,7 +1799,7 @@
- VariantBenchmarkRunOutputGenerator
+ VariantBenchmarkRunOutputGenerator
@@ -1755,8 +1810,8 @@
-
- Bases: BenchmarkRunOutputGenerator
+
+ Bases: BenchmarkRunOutputGenerator
Subclass of BenchmarkRunOutputGenerator specialised
@@ -1764,6 +1819,8 @@
- prioritisation_type_file_prefixprioritisation_type_file_prefix
str
- Prefix for the variant prioritisation type file.
-Defaults to VARIANT_PLOT_FILE_PREFIX.
+
+
Prefix for the variant prioritisation type file.
+Defaults to VARIANT_PLOT_FILE_PREFIX.
+
- y_labely_label
str
- Label for the y-axis in variant prioritisation benchmarking outputs.
-Defaults to VARIANT_PLOT_Y_LABEL.
+
+
Label for the y-axis in variant prioritisation benchmarking outputs.
+Defaults to VARIANT_PLOT_Y_LABEL.
+
- generate_benchmark_run_resultsgenerate_benchmark_run_results
Callable
- Callable to generate variant prioritisation
+
+
+
Callable to generate variant prioritisation
benchmark run results. Defaults to benchmark_variant_prioritisation.
Takes parameters: input and results directory, score order, threshold, rank comparison,
-and returns BenchmarkRunResults.
+and returns BenchmarkRunResults.
+
+
- stats_comparison_file_suffixstats_comparison_file_suffix
str
- Suffix for the variant rank comparison file.
-Defaults to "-variant_summary.tsv".
+
+
Suffix for the variant rank comparison file.
+Defaults to "-variant_summary.tsv".
+
-
-
- Source code in src/pheval/analyse/benchmark_generator.py
- 71
+
+ Source code in src/pheval/analyse/benchmark_generator.py
+ 71
72
73
74
@@ -1872,7 +1944,7 @@ ] = benchmark_variant_prioritisation
stats_comparison_file_suffix : str = "-variant_summary.tsv"
+
@@ -1892,6 +1964,7 @@
- src.pheval.analyse.benchmarking_data
+ benchmarking_data
@@ -1214,7 +1214,7 @@
- src.pheval.analyse.benchmarking_data
+ benchmarking_data
@@ -1251,6 +1251,7 @@
Benchmarking data
+
@@ -1270,7 +1271,7 @@
Benchmarking data
- BenchmarkRunResults
+ BenchmarkRunResults
@@ -1285,6 +1286,8 @@ ranks
dict
- Dictionary containing recorded ranks for samples.
+
+
Dictionary containing recorded ranks for samples.
+
- rank_statsrank_stats
RankStats
- Statistics related to benchmark.
+
+
Statistics related to benchmark.
+
- results_dirresults_dir
Path
- Path to the result directory. Defaults to None.
+
+
Path to the result directory. Defaults to None.
+
- benchmark_namebenchmark_name
str
- Name of the benchmark run. Defaults to None.
+
+
Name of the benchmark run. Defaults to None.
+
-
-
- Source code in src/pheval/analyse/benchmarking_data.py
- 8
+
+ Source code in src/pheval/analyse/benchmarking_data.py
+ 8
9
10
11
@@ -1363,7 +1381,7 @@ results_dir: Path = None
benchmark_name : str = None
+
@@ -1383,6 +1401,7 @@
- src.pheval.analyse.binary_classification_stats
+ binary_classification_stats
@@ -548,105 +548,105 @@
- accuracy()
+ accuracy
- add_classification()
+ add_classification
- add_classification_for_known_entities()
+ add_classification_for_known_entities
- add_classification_for_other_entities()
+ add_classification_for_other_entities
- add_labels_and_scores()
+ add_labels_and_scores
- f1_score()
+ f1_score
- false_discovery_rate()
+ false_discovery_rate
- false_negative_rate()
+ false_negative_rate
- false_positive_rate()
+ false_positive_rate
- matthews_correlation_coefficient()
+ matthews_correlation_coefficient
- negative_predictive_value()
+ negative_predictive_value
- precision()
+ precision
- remove_relevant_ranks()
+ remove_relevant_ranks
- sensitivity()
+ sensitivity
- specificity()
+ specificity
@@ -1325,7 +1325,7 @@
- src.pheval.analyse.binary_classification_stats
+ binary_classification_stats
@@ -1340,105 +1340,105 @@
- accuracy()
+ accuracy
- add_classification()
+ add_classification
- add_classification_for_known_entities()
+ add_classification_for_known_entities
- add_classification_for_other_entities()
+ add_classification_for_other_entities
- add_labels_and_scores()
+ add_labels_and_scores
- f1_score()
+ f1_score
- false_discovery_rate()
+ false_discovery_rate
- false_negative_rate()
+ false_negative_rate
- false_positive_rate()
+ false_positive_rate
- matthews_correlation_coefficient()
+ matthews_correlation_coefficient
- negative_predictive_value()
+ negative_predictive_value
- precision()
+ precision
- remove_relevant_ranks()
+ remove_relevant_ranks
- sensitivity()
+ sensitivity
- specificity()
+ specificity
@@ -1473,6 +1473,7 @@
Binary classification stats
+
@@ -1492,7 +1493,7 @@
Binary classification stats
- BinaryClassificationStats
+ BinaryClassificationStats
@@ -1507,6 +1508,8 @@
- true_positivestrue_positives
int
- The count of true positive instances - i.e., the number of known entities
-ranked 1 in the results.
+
+
The count of true positive instances - i.e., the number of known entities
+ranked 1 in the results.
+
- true_negativestrue_negatives
int
- The count of true negative instances - i.e., the number of non-relevant entities
-ranked at a position other than 1 in the results.
+
+
The count of true negative instances - i.e., the number of non-relevant entities
+ranked at a position other than 1 in the results.
+
- false_positivesfalse_positives
int
- The count of false positive instances - i.e., the number of non-relevant entities
-ranked at position 1 in the results.
+
+
The count of false positive instances - i.e., the number of non-relevant entities
+ranked at position 1 in the results.
+
- false_negativesfalse_negatives
int
- The count of false negative instances - i.e., the number of known entities
-ranked at a position other than 1 in the results.
+
+
The count of false negative instances - i.e., the number of known entities
+ranked at a position other than 1 in the results.
+
-
-
- Source code in src/pheval/analyse/binary_classification_stats.py
- 12
+
+ Source code in src/pheval/analyse/binary_classification_stats.py
+ 12
13
14
15
@@ -2191,7 +2209,7 @@ else 0.0
)
+
@@ -2205,12 +2223,13 @@
-accuracy () accuracy ()
@@ -2220,6 +2239,8 @@ float
float
- The Accuracy of the model, calculated as the sum of true positives and true negatives divided by
+
+
The Accuracy of the model, calculated as the sum of true positives and true negatives divided by
+
float
- the sum of true positives, false positives, true negatives, and false negatives.
+
+
the sum of true positives, false positives, true negatives, and false negatives.
+
float
- Returns 0.0 if the total sum of counts is zero.
+
+
Returns 0.0 if the total sum of counts is zero.
+
-
- Source code in src/pheval/analyse/binary_classification_stats.py
- 250
+
+ Source code in src/pheval/analyse/binary_classification_stats.py
+ 250
251
252
253
@@ -2308,63 +2341,34 @@ else 0.0
)
+
-add_classification ( pheval_results , relevant_ranks ) add_classification ( pheval_results , relevant_ranks )
-
Update binary classification metrics for known and unknown entities based on their ranks.
-
-
Parameters:
-
-
-
- Name
- Type
- Description
- Default
-
-
-
-
- pheval_results
- Union [List [RankedPhEvalGeneResult ], List [RankedPhEvalVariantResult ], List [RankedPhEvalDiseaseResult ]]
- (Union[List[RankedPhEvalGeneResult], List[RankedPhEvalVariantResult], List[RankedPhEvalDiseaseResult]]):
- The list of all pheval results.
- required
-
-
-
- relevant_ranks
- List [int]
- A list of the ranks associated with the known entities.
- required
-
-
-
-
+
Update binary classification metrics for known and unknown entities based on their ranks.
+Args:
+ pheval_results:
+ (Union[List[RankedPhEvalGeneResult], List[RankedPhEvalVariantResult], List[RankedPhEvalDiseaseResult]]):
+ The list of all pheval results.
+ relevant_ranks (List[int]): A list of the ranks associated with the known entities.
-
- Source code in src/pheval/analyse/binary_classification_stats.py
- 114
+
+ Source code in src/pheval/analyse/binary_classification_stats.py
+ 114
115
116
117
@@ -2408,17 +2412,18 @@ )
self . add_labels_and_scores ( pheval_results , relevant_ranks )
+
-add_classification_for_known_entities ( relevant_ranks ) add_classification_for_known_entities ( relevant_ranks )
@@ -2427,6 +2432,8 @@
List [int] A list of the ranks associated with the known entities.
+
+
A list of the ranks associated with the known entities.
+
required
@@ -2451,9 +2462,9 @@
- Source code in src/pheval/analyse/binary_classification_stats.py
- 63
+
+ Source code in src/pheval/analyse/binary_classification_stats.py
+ 63
64
65
66
@@ -2477,17 +2488,18 @@ elif rank != 1 :
self . false_negatives += 1
+
-add_classification_for_other_entities ( ranks ) add_classification_for_other_entities ( ranks )
@@ -2496,6 +2508,8 @@
List [int] A list of the ranks for all other entities.
+
+
A list of the ranks for all other entities.
+
required
@@ -2520,9 +2538,9 @@
- Source code in src/pheval/analyse/binary_classification_stats.py
- 76
+
+ Source code in src/pheval/analyse/binary_classification_stats.py
+ 76
77
78
79
@@ -2546,17 +2564,18 @@ elif rank != 1 :
self . true_negatives += 1
+
-add_labels_and_scores ( pheval_results , relevant_ranks ) add_labels_and_scores ( pheval_results , relevant_ranks )
@@ -2565,6 +2584,8 @@
List [int] A list of the ranks associated with the known entities.
+
+
A list of the ranks associated with the known entities.
+
required
@@ -2589,9 +2614,9 @@
- Source code in src/pheval/analyse/binary_classification_stats.py
- 89
+
+ Source code in src/pheval/analyse/binary_classification_stats.py
+ 89
90
91
92
@@ -2639,17 +2664,18 @@ self. labels . append ( label )
relevant_ranks_copy . remove ( result . rank ) if label == 1 else None
+
-f1_score () f1_score ()
@@ -2660,6 +2686,8 @@ float
float
- The F1 Score of the model, calculated as 2 * TP / (2 * TP + FP + FN).
+
+
The F1 Score of the model, calculated as 2 * TP / (2 * TP + FP + FN).
+
float
- Returns 0.0 if the denominator is zero.
+
+
Returns 0.0 if the denominator is zero.
+
-
- Source code in src/pheval/analyse/binary_classification_stats.py
- 279
+
+ Source code in src/pheval/analyse/binary_classification_stats.py
+ 279
280
281
282
@@ -2720,17 +2756,18 @@ else 0.0
)
+
-false_discovery_rate () false_discovery_rate ()
@@ -2740,6 +2777,8 @@ float
float
- The False Discovery Rate of the model, calculated as false positives divided by the sum of
+
+
The False Discovery Rate of the model, calculated as false positives divided by the sum of
+
float
- false positives and true positives. Returns 0.0 if both false positives and true positives are zero.
+
+
false positives and true positives. Returns 0.0 if both false positives and true positives are zero.
+
-
- Source code in src/pheval/analyse/binary_classification_stats.py
- 218
+
+ Source code in src/pheval/analyse/binary_classification_stats.py
+ 218
219
220
221
@@ -2796,17 +2843,18 @@ else 0.0
)
+
-false_negative_rate () false_negative_rate ()
@@ -2816,6 +2864,8 @@ float
float
- The False Negative Rate of the model, calculated as false negatives divided by the sum of
+
+
The False Negative Rate of the model, calculated as false negatives divided by the sum of
+
float
- false negatives and true positives. Returns 0.0 if both false negatives and true positives are zero.
+
+
false negatives and true positives. Returns 0.0 if both false negatives and true positives are zero.
+
-
- Source code in src/pheval/analyse/binary_classification_stats.py
- 234
+
+ Source code in src/pheval/analyse/binary_classification_stats.py
+ 234
235
236
237
@@ -2872,17 +2930,18 @@ else 0.0
)
+
-false_positive_rate () false_positive_rate ()
@@ -2892,6 +2951,8 @@ float
float
- The False Positive Rate of the model, calculated as false positives divided by the sum of
+
+
The False Positive Rate of the model, calculated as false positives divided by the sum of
+
float
- false positives and true negatives. Returns 0.0 if both false positives and true negatives are zero.
+
+
false positives and true negatives. Returns 0.0 if both false positives and true negatives are zero.
+
-
- Source code in src/pheval/analyse/binary_classification_stats.py
- 202
+
+ Source code in src/pheval/analyse/binary_classification_stats.py
+ 202
203
204
205
@@ -2948,17 +3017,18 @@ else 0.0
)
+
-matthews_correlation_coefficient () matthews_correlation_coefficient ()
@@ -2968,6 +3038,8 @@ float
float
- The Matthews Correlation Coefficient of the model, calculated as
+
+
The Matthews Correlation Coefficient of the model, calculated as
+
float
- ((TP * TN) - (FP * FN)) / sqrt((TP + FP) * (TP + FN) * (TN + FP) * (TN + FN)).
+
+
((TP * TN) - (FP * FN)) / sqrt((TP + FP) * (TP + FN) * (TN + FP) * (TN + FN)).
+
float
- Returns 0.0 if the denominator is zero.
+
+
Returns 0.0 if the denominator is zero.
+
-
- Source code in src/pheval/analyse/binary_classification_stats.py
- 297
+
+ Source code in src/pheval/analyse/binary_classification_stats.py
+ 297
298
299
300
@@ -3066,17 +3150,18 @@ else 0.0
)
+
-negative_predictive_value () negative_predictive_value ()
@@ -3086,6 +3171,8 @@ float
float
- The Negative Predictive Value of the model, calculated as true negatives divided by the sum of
+
+
The Negative Predictive Value of the model, calculated as true negatives divided by the sum of
+
float
- true negatives and false negatives. Returns 0.0 if both true negatives and false negatives are zero.
+
+
true negatives and false negatives. Returns 0.0 if both true negatives and false negatives are zero.
+
-
- Source code in src/pheval/analyse/binary_classification_stats.py
- 186
+
+ Source code in src/pheval/analyse/binary_classification_stats.py
+ 186
187
188
189
@@ -3142,17 +3237,18 @@ else 0.0
)
+
-precision () precision ()
@@ -3163,6 +3259,8 @@ float
float
- The precision of the model, calculated as true positives divided by the sum of true positives
+
+
The precision of the model, calculated as true positives divided by the sum of true positives
+
float
- and false positives. Returns 0.0 if both true positives and false positives are zero.
+
+
and false positives. Returns 0.0 if both true positives and false positives are zero.
+
-
- Source code in src/pheval/analyse/binary_classification_stats.py
- 169
+
+ Source code in src/pheval/analyse/binary_classification_stats.py
+ 169
170
171
172
@@ -3221,17 +3327,18 @@ else 0.0
)
+
-remove_relevant_ranks ( pheval_results , relevant_ranks ) remove_relevant_ranks ( pheval_results , relevant_ranks )
staticmethod
- Remove the relevant entity ranks from all result ranks
+ Remove the relevant entity ranks from all result ranks
+Args:
+ pheval_results:
+ (Union[List[RankedPhEvalGeneResult], List[RankedPhEvalVariantResult], List[RankedPhEvalDiseaseResult]]):
+ The list of all pheval results.
+ relevant_ranks (List[int]): A list of the ranks associated with the known entities.
+
- Parameters:
-
-
-
- Name
- Type
- Description
- Default
-
-
-
-
- pheval_results
- Union [List [RankedPhEvalGeneResult ], List [RankedPhEvalVariantResult ], List [RankedPhEvalDiseaseResult ]]
- (Union[List[RankedPhEvalGeneResult], List[RankedPhEvalVariantResult], List[RankedPhEvalDiseaseResult]]):
- The list of all pheval results.
- required
-
-
-
- relevant_ranks
- List [int]
- A list of the ranks associated with the known entities.
- required
-
-
-
-
Returns:
@@ -3292,14 +3371,18 @@ List[int]
- List[int]: A list of the ranks with the relevant entity ranks removed.
+
+
List[int]: A list of the ranks with the relevant entity ranks removed.
+
-
- Source code in src/pheval/analyse/binary_classification_stats.py
- 35
+
+ Source code in src/pheval/analyse/binary_classification_stats.py
+ 35
36
37
38
@@ -3353,17 +3436,18 @@ continue
return all_result_ranks
+
-sensitivity () sensitivity ()
@@ -3373,6 +3457,8 @@ float
float
- The sensitivity of the model, calculated as true positives divided by the sum of true positives
+
+
The sensitivity of the model, calculated as true positives divided by the sum of true positives
+
float
- and false negatives. Returns 0 if both true positives and false negatives are zero.
+
+
and false negatives. Returns 0 if both true positives and false negatives are zero.
+
-
- Source code in src/pheval/analyse/binary_classification_stats.py
- 137
+
+ Source code in src/pheval/analyse/binary_classification_stats.py
+ 137
138
139
140
@@ -3429,17 +3523,18 @@ else 0.0
)
+
-specificity () specificity ()
@@ -3449,6 +3544,8 @@ float
float
- The specificity of the model, calculated as true negatives divided by the sum of true negatives
+
+
The specificity of the model, calculated as true negatives divided by the sum of true negatives
+
float
- and false positives. Returns 0.0 if both true negatives and false positives are zero.
+
+
and false positives. Returns 0.0 if both true negatives and false positives are zero.
+
-
- Source code in src/pheval/analyse/binary_classification_stats.py
- 153
+
+ Source code in src/pheval/analyse/binary_classification_stats.py
+ 153
154
155
156
@@ -3505,7 +3610,7 @@ else 0.0
)
+
- src.pheval.analyse.disease_prioritisation_analysis
+ disease_prioritisation_analysis
@@ -562,14 +562,14 @@
- __init__()
+ __init__
- assess_disease_prioritisation()
+ assess_disease_prioritisation
@@ -581,14 +581,14 @@
- assess_phenopacket_disease_prioritisation()
+ assess_phenopacket_disease_prioritisation
- benchmark_disease_prioritisation()
+ benchmark_disease_prioritisation
@@ -1248,7 +1248,7 @@
- src.pheval.analyse.disease_prioritisation_analysis
+ disease_prioritisation_analysis
@@ -1263,14 +1263,14 @@
- __init__()
+ __init__
- assess_disease_prioritisation()
+ assess_disease_prioritisation
@@ -1282,14 +1282,14 @@
- assess_phenopacket_disease_prioritisation()
+ assess_phenopacket_disease_prioritisation
- benchmark_disease_prioritisation()
+ benchmark_disease_prioritisation
@@ -1319,6 +1319,7 @@ Disease prioritisation analysis
+
@@ -1338,7 +1339,7 @@
Disease prioritisation analysis
- AssessDiseasePrioritisation
+ AssessDiseasePrioritisation
@@ -1349,10 +1350,9 @@
- Source code in src/pheval/analyse/disease_prioritisation_analysis.py
- 17
+
+ Source code in src/pheval/analyse/disease_prioritisation_analysis.py
+ 17
18
19
20
@@ -1714,7 +1714,7 @@ self. standardised_disease_results , relevant_ranks
)
+
@@ -1728,12 +1728,13 @@
-__init__ ( phenopacket_path , results_dir , standardised_disease_results , threshold , score_order , proband_diseases ) __init__ ( phenopacket_path , results_dir , standardised_disease_results , threshold , score_order , proband_diseases )
@@ -1742,6 +1743,8 @@
Path Path to the phenopacket file
+
+
Path to the phenopacket file
+
required
@@ -1768,7 +1775,11 @@ Path
- Path to the results directory
+
+
Path to the results directory
+
required
@@ -1778,7 +1789,11 @@ List[RankedPhEvalDiseaseResult ]
- List of ranked PhEval disease results
+
+
List of ranked PhEval disease results
+
required
@@ -1788,7 +1803,11 @@
+ Threshold for scores
+
+
required
@@ -1798,7 +1817,11 @@
+ Score order for results, either ascending or descending
+
+
required
@@ -1808,7 +1831,11 @@ List[ProbandDisease ]
- List of proband diseases
+
+
List of proband diseases
+
required
@@ -1816,9 +1843,9 @@
- Source code in src/pheval/analyse/disease_prioritisation_analysis.py
- 20
+
+ Source code in src/pheval/analyse/disease_prioritisation_analysis.py
+ 20
21
22
23
@@ -1872,17 +1899,18 @@ self. score_order = score_order
self . proband_diseases = proband_diseases
+
-assess_disease_prioritisation ( rank_stats , rank_records , binary_classification_stats ) assess_disease_prioritisation ( rank_stats , rank_records , binary_classification_stats )
@@ -1893,6 +1921,8 @@
RankStats RankStats class instance
+
+
RankStats class instance
+
required
@@ -1919,7 +1953,11 @@ defaultdict
- A defaultdict to store the correct ranked results.
+
+
A defaultdict to store the correct ranked results.
+
required
@@ -1929,7 +1967,11 @@ BinaryClassificationStats
- BinaryClassificationStats class instance.
+
+
BinaryClassificationStats class instance.
+
required
@@ -1937,9 +1979,9 @@
- Source code in src/pheval/analyse/disease_prioritisation_analysis.py
- 149
+
+ Source code in src/pheval/analyse/disease_prioritisation_analysis.py
+ 149
150
151
152
@@ -2037,7 +2079,7 @@ self. standardised_disease_results , relevant_ranks
)
+
-assess_phenopacket_disease_prioritisation ( phenopacket_path , score_order , results_dir_and_input , threshold , disease_rank_stats , disease_rank_comparison , disease_binary_classification_stats ) assess_phenopacket_disease_prioritisation ( phenopacket_path , score_order , results_dir_and_input , threshold , disease_rank_stats , disease_rank_comparison , disease_binary_classification_stats )
@@ -2066,6 +2110,8 @@
Path Path to the Phenopacket.
+
+
Path to the Phenopacket.
+
required
@@ -2092,7 +2142,11 @@
+ The order in which scores are arranged, either ascending or descending.
+
+
required
@@ -2102,7 +2156,11 @@ TrackInputOutputDirectories
- Input and output directories.
+
+
Input and output directories.
+
required
@@ -2112,7 +2170,11 @@
+ Threshold for assessment.
+
+
required
@@ -2122,7 +2184,11 @@ RankStats
- RankStats class instance.
+
+
RankStats class instance.
+
required
@@ -2132,7 +2198,11 @@ defaultdict
- Default dictionary for disease rank comparisons.
+
+
Default dictionary for disease rank comparisons.
+
required
@@ -2142,7 +2212,11 @@ BinaryClassificationStats
- BinaryClassificationStats class instance.
+
+
BinaryClassificationStats class instance.
+
required
@@ -2150,9 +2224,9 @@
- Source code in src/pheval/analyse/disease_prioritisation_analysis.py
- 215
+
+ Source code in src/pheval/analyse/disease_prioritisation_analysis.py
+ 215
216
217
218
@@ -2226,17 +2300,18 @@ disease_rank_stats, disease_rank_comparison , disease_binary_classification_stats
)
+
-benchmark_disease_prioritisation ( results_directory_and_input , score_order , threshold , disease_rank_comparison ) benchmark_disease_prioritisation ( results_directory_and_input , score_order , threshold , disease_rank_comparison )
@@ -2245,6 +2320,8 @@
TrackInputOutputDirectories Input and output directories.
+
+
Input and output directories.
+
required
@@ -2271,7 +2352,11 @@
+ The order in which scores are arranged.
+
+
required
@@ -2281,7 +2366,11 @@
+ Threshold for assessment.
+
+
required
@@ -2291,7 +2380,11 @@ defaultdict
- Default dictionary for disease rank comparisons.
+
+
Default dictionary for disease rank comparisons.
+
required
@@ -2299,6 +2392,8 @@
BenchmarkRunResults
- An object containing benchmarking results for disease prioritisation,
+
+
An object containing benchmarking results for disease prioritisation,
+
- including ranks and rank statistics for the benchmarked directory.
+
+
including ranks and rank statistics for the benchmarked directory.
+
-
- Source code in src/pheval/analyse/disease_prioritisation_analysis.py
- 254
+
+ Source code in src/pheval/analyse/disease_prioritisation_analysis.py
+ 254
255
256
257
@@ -2397,7 +2500,7 @@ binary_classification_stats= disease_binary_classification_stats ,
)
+
- src.pheval.analyse.gene_prioritisation_analysis
+ gene_prioritisation_analysis
@@ -576,14 +576,14 @@
- __init__()
+ __init__
- assess_gene_prioritisation()
+ assess_gene_prioritisation
@@ -595,14 +595,14 @@
- assess_phenopacket_gene_prioritisation()
+ assess_phenopacket_gene_prioritisation
- benchmark_gene_prioritisation()
+ benchmark_gene_prioritisation
@@ -1248,7 +1248,7 @@
- src.pheval.analyse.gene_prioritisation_analysis
+ gene_prioritisation_analysis
@@ -1263,14 +1263,14 @@
- __init__()
+ __init__
- assess_gene_prioritisation()
+ assess_gene_prioritisation
@@ -1282,14 +1282,14 @@
- assess_phenopacket_gene_prioritisation()
+ assess_phenopacket_gene_prioritisation
- benchmark_gene_prioritisation()
+ benchmark_gene_prioritisation
@@ -1319,6 +1319,7 @@ Gene prioritisation analysis
+
@@ -1338,7 +1339,7 @@
Gene prioritisation analysis
- AssessGenePrioritisation
+ AssessGenePrioritisation
@@ -1349,10 +1350,9 @@
- Source code in src/pheval/analyse/gene_prioritisation_analysis.py
- 19
+
+ Source code in src/pheval/analyse/gene_prioritisation_analysis.py
+ 19
20
21
22
@@ -1760,7 +1760,7 @@ pheval_results= self . standardised_gene_results , relevant_ranks = relevant_ranks
)
+
@@ -1774,12 +1774,13 @@
-__init__ ( phenopacket_path , results_dir , standardised_gene_results , threshold , score_order , proband_causative_genes ) __init__ ( phenopacket_path , results_dir , standardised_gene_results , threshold , score_order , proband_causative_genes )
@@ -1788,6 +1789,8 @@
Path Path to the phenopacket file
+
+
Path to the phenopacket file
+
required
@@ -1814,7 +1821,11 @@ Path
- Path to the results directory
+
+
Path to the results directory
+
required
@@ -1824,7 +1835,11 @@ List[RankedPhEvalGeneResult ]
- List of ranked PhEval gene results
+
+
List of ranked PhEval gene results
+
required
@@ -1834,7 +1849,11 @@
+ Threshold for scores
+
+
required
@@ -1844,7 +1863,11 @@
+ Score order for results, either ascending or descending
+
+
required
@@ -1854,7 +1877,11 @@ List[ProbandCausativeGene ]
- List of proband causative genes
+
+
List of proband causative genes
+
required
@@ -1862,9 +1889,9 @@
- Source code in src/pheval/analyse/gene_prioritisation_analysis.py
- 22
+
+ Source code in src/pheval/analyse/gene_prioritisation_analysis.py
+ 22
23
24
25
@@ -1916,17 +1943,18 @@ self. score_order = score_order
self . proband_causative_genes = proband_causative_genes
+
-assess_gene_prioritisation ( rank_stats , rank_records , binary_classification_stats ) assess_gene_prioritisation ( rank_stats , rank_records , binary_classification_stats )
@@ -1937,6 +1965,8 @@
RankStats RankStats class instance
+
+
RankStats class instance
+
required
@@ -1963,7 +1997,11 @@ defaultdict
- A defaultdict to store the correct ranked results.
+
+
A defaultdict to store the correct ranked results.
+
required
@@ -1973,7 +2011,11 @@ BinaryClassificationStats
- BinaryClassificationStats class instance.
+
+
BinaryClassificationStats class instance.
+
required
@@ -1981,9 +2023,9 @@
- Source code in src/pheval/analyse/gene_prioritisation_analysis.py
- 163
+
+ Source code in src/pheval/analyse/gene_prioritisation_analysis.py
+ 163
164
165
166
@@ -2103,7 +2145,7 @@ pheval_results= self . standardised_gene_results , relevant_ranks = relevant_ranks
)
+
-assess_phenopacket_gene_prioritisation ( phenopacket_path , score_order , results_dir_and_input , threshold , gene_rank_stats , gene_rank_comparison , gene_binary_classification_stats ) assess_phenopacket_gene_prioritisation ( phenopacket_path , score_order , results_dir_and_input , threshold , gene_rank_stats , gene_rank_comparison , gene_binary_classification_stats )
@@ -2132,6 +2176,8 @@
Path Path to the Phenopacket.
+
+
Path to the Phenopacket.
+
required
@@ -2158,7 +2208,11 @@
+ The order in which scores are arranged, either ascending or descending.
+
+
required
@@ -2168,7 +2222,11 @@ TrackInputOutputDirectories
- Input and output directories.
+
+
Input and output directories.
+
required
@@ -2178,7 +2236,11 @@
+ Threshold for assessment.
+
+
required
@@ -2188,7 +2250,11 @@ RankStats
- RankStats class instance.
+
+
RankStats class instance.
+
required
@@ -2198,7 +2264,11 @@ defaultdict
- Default dictionary for gene rank comparisons.
+
+
Default dictionary for gene rank comparisons.
+
required
@@ -2208,7 +2278,11 @@ BinaryClassificationStats
- BinaryClassificationStats class instance.
+
+
BinaryClassificationStats class instance.
+
required
@@ -2216,9 +2290,9 @@
- Source code in src/pheval/analyse/gene_prioritisation_analysis.py
- 239
+
+ Source code in src/pheval/analyse/gene_prioritisation_analysis.py
+ 239
240
241
242
@@ -2292,17 +2366,18 @@ gene_rank_stats, gene_rank_comparison , gene_binary_classification_stats
)
+
-benchmark_gene_prioritisation ( results_directory_and_input , score_order , threshold , gene_rank_comparison ) benchmark_gene_prioritisation ( results_directory_and_input , score_order , threshold , gene_rank_comparison )
@@ -2319,9 +2394,9 @@
- Source code in src/pheval/analyse/gene_prioritisation_analysis.py
- 278
+
+ Source code in src/pheval/analyse/gene_prioritisation_analysis.py
+ 278
279
280
281
@@ -2391,7 +2466,7 @@ binary_classification_stats= gene_binary_classification_stats ,
)
+
- src.pheval.analyse.generate_plots
+ generate_plots
@@ -590,49 +590,49 @@
- __init__()
+ __init__
- generate_cumulative_bar()
+ generate_cumulative_bar
- generate_non_cumulative_bar()
+ generate_non_cumulative_bar
- generate_precision_recall()
+ generate_precision_recall
- generate_roc_curve()
+ generate_roc_curve
- generate_stacked_bar_plot()
+ generate_stacked_bar_plot
- return_benchmark_name()
+ return_benchmark_name
@@ -644,21 +644,21 @@
- generate_plots()
+ generate_plots
- generate_plots_from_benchmark_summary_tsv()
+ generate_plots_from_benchmark_summary_tsv
- trim_corpus_results_directory_suffix()
+ trim_corpus_results_directory_suffix
@@ -1290,7 +1290,7 @@
- src.pheval.analyse.generate_plots
+ generate_plots
@@ -1305,49 +1305,49 @@
- __init__()
+ __init__
- generate_cumulative_bar()
+ generate_cumulative_bar
- generate_non_cumulative_bar()
+ generate_non_cumulative_bar
- generate_precision_recall()
+ generate_precision_recall
- generate_roc_curve()
+ generate_roc_curve
- generate_stacked_bar_plot()
+ generate_stacked_bar_plot
- return_benchmark_name()
+ return_benchmark_name
@@ -1359,21 +1359,21 @@
- generate_plots()
+ generate_plots
- generate_plots_from_benchmark_summary_tsv()
+ generate_plots_from_benchmark_summary_tsv
- trim_corpus_results_directory_suffix()
+ trim_corpus_results_directory_suffix
@@ -1403,6 +1403,7 @@ Generate plots
+
@@ -1422,7 +1423,7 @@
Generate plots
- PlotGenerator
+ PlotGenerator
@@ -1433,10 +1434,9 @@
Class to generate plots.
-
-
- Source code in src/pheval/analyse/generate_plots.py
- 37
+
+ Source code in src/pheval/analyse/generate_plots.py
+ 37
38
39
40
@@ -2318,7 +2318,7 @@ bbox_inches= "tight" ,
)
+
@@ -2332,30 +2332,29 @@
-__init__ () __init__ ()
-
Initialise the PlotGenerator class.
-
-
- Note
- self.stats will be used to store statistics data.
-self.mrr will store Mean Reciprocal Rank (MRR) values.
-Matplotlib settings are configured to remove the right and top axes spines
-for generated plots.
-
-
- Source code in src/pheval/analyse/generate_plots.py
- 53
+ Initialise the PlotGenerator class.
+Note:
+ self.stats will be used to store statistics data.
+ self.mrr will store Mean Reciprocal Rank (MRR) values.
+ Matplotlib settings are configured to remove the right and top axes spines
+ for generated plots.
+
+
+ Source code in src/pheval/analyse/generate_plots.py
+ 53
54
55
56
@@ -2383,17 +2382,18 @@ matplotlib. rcParams [ "axes.spines.right" ] = False
matplotlib . rcParams [ "axes.spines.top" ] = False
+
-generate_cumulative_bar ( benchmarking_results , benchmark_generator , title = None ) generate_cumulative_bar ( benchmarking_results , benchmark_generator , title = None )
@@ -2402,6 +2402,8 @@
Generate a cumulative bar plot.
+
+
Parameters:
@@ -2418,7 +2420,11 @@
List [BenchmarkRunResults ]List of benchmarking results for multiple runs.
+
+
List of benchmarking results for multiple runs.
+
required
@@ -2428,7 +2434,11 @@
BenchmarkRunOutputGenerator Object containing benchmarking output generation details.
+
+
Object containing benchmarking output generation details.
+
required
@@ -2438,7 +2448,11 @@
str
- Title for the generated plot. Defaults to None.
+
+
Title for the generated plot. Defaults to None.
+
None
@@ -2446,9 +2460,9 @@
-
- Source code in src/pheval/analyse/generate_plots.py
- 253
+
+ Source code in src/pheval/analyse/generate_plots.py
+ 253
254
255
256
@@ -2528,17 +2542,18 @@ bbox_inches= "tight" ,
)
+
-generate_non_cumulative_bar ( benchmarking_results , benchmark_generator , title = None ) generate_non_cumulative_bar ( benchmarking_results , benchmark_generator , title = None )
@@ -2547,6 +2562,8 @@
List [BenchmarkRunResults ] List of benchmarking results for multiple runs.
+
+
List of benchmarking results for multiple runs.
+
required
@@ -2573,7 +2594,11 @@ BenchmarkRunOutputGenerator
- Object containing benchmarking output generation details.
+
+
Object containing benchmarking output generation details.
+
required
@@ -2583,7 +2608,11 @@
+ Title for the generated plot. Defaults to None.
+
+
None
@@ -2591,9 +2620,9 @@
- Source code in src/pheval/analyse/generate_plots.py
- 437
+
+ Source code in src/pheval/analyse/generate_plots.py
+ 437
438
439
440
@@ -2675,17 +2704,18 @@ bbox_inches= "tight" ,
)
+
-generate_precision_recall ( benchmarking_results , benchmark_generator ) generate_precision_recall ( benchmarking_results , benchmark_generator )
@@ -2694,6 +2724,8 @@
List [BenchmarkRunResults ] List of benchmarking results for multiple runs.
+
+
List of benchmarking results for multiple runs.
+
required
@@ -2720,7 +2756,11 @@ BenchmarkRunOutputGenerator
- Object containing benchmarking output generation details.
+
+
Object containing benchmarking output generation details.
+
required
@@ -2728,9 +2768,9 @@
- Source code in src/pheval/analyse/generate_plots.py
- 399
+
+ Source code in src/pheval/analyse/generate_plots.py
+ 399
400
401
402
@@ -2804,17 +2844,18 @@ bbox_inches= "tight" ,
)
+
-generate_roc_curve ( benchmarking_results , benchmark_generator ) generate_roc_curve ( benchmarking_results , benchmark_generator )
@@ -2823,6 +2864,8 @@
Generate and plot Receiver Operating Characteristic (ROC) curves for binary classification benchmark results.
+
+
Parameters:
@@ -2839,7 +2882,11 @@
List [BenchmarkRunResults ]List of benchmarking results for multiple runs.
+
+
List of benchmarking results for multiple runs.
+
required
@@ -2849,7 +2896,11 @@
BenchmarkRunOutputGenerator Object containing benchmarking output generation details.
+
+
Object containing benchmarking output generation details.
+
required
@@ -2857,9 +2908,9 @@
-
- Source code in src/pheval/analyse/generate_plots.py
- 361
+
+ Source code in src/pheval/analyse/generate_plots.py
+ 361
362
363
364
@@ -2933,17 +2984,18 @@ bbox_inches= "tight" ,
)
+
-generate_stacked_bar_plot ( benchmarking_results , benchmark_generator , title = None ) generate_stacked_bar_plot ( benchmarking_results , benchmark_generator , title = None )
@@ -2952,6 +3004,8 @@
List [BenchmarkRunResults ] List of benchmarking results for multiple runs.
+
+
List of benchmarking results for multiple runs.
+
required
@@ -2978,7 +3036,11 @@ BenchmarkRunOutputGenerator
- Object containing benchmarking output generation details.
+
+
Object containing benchmarking output generation details.
+
required
@@ -2988,7 +3050,11 @@
+ Title for the generated plot. Defaults to None.
+
+
None
@@ -2996,9 +3062,9 @@
- Source code in src/pheval/analyse/generate_plots.py
- 144
+
+ Source code in src/pheval/analyse/generate_plots.py
+ 144
145
146
147
@@ -3108,17 +3174,18 @@ bbox_inches= "tight" ,
)
+
-return_benchmark_name ( benchmark_result ) return_benchmark_name ( benchmark_result )
@@ -3127,6 +3194,8 @@
Return the benchmark name for a run.
+
+
Parameters:
@@ -3143,7 +3212,11 @@
BenchmarkRunResults The benchmarking results for a run.
+
+
The benchmarking results for a run.
+
required
@@ -3151,6 +3224,8 @@
+
+
Returns:
@@ -3164,14 +3239,18 @@ str
str
- The benchmark name obtained from the given BenchmarkRunResults instance.
+
+
The benchmark name obtained from the given BenchmarkRunResults instance.
+
-
- Source code in src/pheval/analyse/generate_plots.py
- 81
+
+ Source code in src/pheval/analyse/generate_plots.py
+ 81
82
83
84
@@ -3201,7 +3280,7 @@ else self . _create_run_identifier ( benchmark_result . results_dir )
)
+
+
+
-generate_plots ( benchmarking_results , benchmark_generator , plot_type , title = None , generate_from_tsv = False ) generate_plots ( benchmarking_results , benchmark_generator , plot_type , title = None , generate_from_tsv = False )
@@ -3230,6 +3311,8 @@ BenchmarkRunResults]
List of benchmarking results for multiple runs.
+
+
List of benchmarking results for multiple runs.
+
required
@@ -3256,7 +3343,11 @@ BenchmarkRunOutputGenerator
- Object containing benchmarking output generation details.
+
+
Object containing benchmarking output generation details.
+
required
@@ -3266,7 +3357,11 @@
+
+
+
Type of plot to be generated ("bar_stacked", "bar_cumulative", "bar_non_cumulative").
+
required
@@ -3276,7 +3371,11 @@
+ Title for the generated plot. Defaults to None.
+
+
None
@@ -3286,7 +3385,11 @@
+ Specify whether to generate plots from the TSV file. Defaults to False.
+
+
False
@@ -3294,9 +3397,9 @@
- Source code in src/pheval/analyse/generate_plots.py
- 480
+
+ Source code in src/pheval/analyse/generate_plots.py
+ 480
481
482
483
@@ -3354,17 +3457,18 @@ elif plot_type == "bar_non_cumulative" :
plot_generator . generate_non_cumulative_bar ( benchmarking_results , benchmark_generator , title )
+
-generate_plots_from_benchmark_summary_tsv ( benchmark_summary_tsv , gene_analysis , variant_analysis , disease_analysis , plot_type , title ) generate_plots_from_benchmark_summary_tsv ( benchmark_summary_tsv , gene_analysis , variant_analysis , disease_analysis , plot_type , title )
@@ -3375,6 +3479,8 @@
Path Path to the summary TSV file containing benchmark results.
+
+
Path to the summary TSV file containing benchmark results.
+
required
@@ -3401,7 +3511,11 @@
+ Flag indicating whether to analyse gene prioritisation.
+
+
required
@@ -3411,7 +3525,11 @@
+ Flag indicating whether to analyse variant prioritisation.
+
+
required
@@ -3421,7 +3539,11 @@
+ Flag indicating whether to analyse disease prioritisation.
+
+
required
@@ -3431,7 +3553,11 @@
+
+
+
Type of plot to be generated ("bar_stacked", "bar_cumulative", "bar_non_cumulative").
+
required
@@ -3441,35 +3567,23 @@
+ Title for the generated plot.
+
-
-
-
Raises:
-
-
-
- Type
- Description
-
-
-
-
- ValueError
+ required
- If an unsupported plot type is specified.
+
Raises:
+ ValueError: If an unsupported plot type is specified.
-
- Source code in src/pheval/analyse/generate_plots.py
- 511
+
+ Source code in src/pheval/analyse/generate_plots.py
+ 511
512
513
514
@@ -3543,17 +3657,18 @@ )
generate_plots ( benchmarking_results , benchmark_generator , plot_type , title , True )
+
-trim_corpus_results_directory_suffix ( corpus_results_directory ) trim_corpus_results_directory_suffix ( corpus_results_directory )
@@ -3562,6 +3677,8 @@
Trim the suffix from the corpus results directory name.
+
+
Parameters:
@@ -3578,7 +3695,11 @@
Path The directory path containing corpus results.
+
+
The directory path containing corpus results.
+
required
@@ -3586,6 +3707,8 @@
+
+
Returns:
@@ -3599,14 +3722,18 @@ Path
Path
- The Path object with the suffix removed from the directory name.
+
+
The Path object with the suffix removed from the directory name.
+
-
- Source code in src/pheval/analyse/generate_plots.py
- 24
+
+ Source code in src/pheval/analyse/generate_plots.py
+ 24
25
26
27
@@ -3628,7 +3755,7 @@ """
return Path ( str ( corpus_results_directory ) . replace ( PHEVAL_RESULTS_DIRECTORY_SUFFIX , "" ))
+
- src.pheval.analyse.generate_summary_outputs
+ generate_summary_outputs
@@ -604,21 +604,21 @@
- __init__()
+ __init__
- generate_comparison_output()
+ generate_comparison_output
- generate_output()
+ generate_output
@@ -630,21 +630,21 @@
- generate_benchmark_comparison_output()
+ generate_benchmark_comparison_output
- generate_benchmark_output()
+ generate_benchmark_output
- merge_results()
+ merge_results
@@ -1262,7 +1262,7 @@
- src.pheval.analyse.generate_summary_outputs
+ generate_summary_outputs
@@ -1277,21 +1277,21 @@
- __init__()
+ __init__
- generate_comparison_output()
+ generate_comparison_output
- generate_output()
+ generate_output
@@ -1303,21 +1303,21 @@
- generate_benchmark_comparison_output()
+ generate_benchmark_comparison_output
- generate_benchmark_output()
+ generate_benchmark_output
- merge_results()
+ merge_results
@@ -1347,6 +1347,7 @@ Generate summary outputs
+
@@ -1366,7 +1367,7 @@
Generate summary outputs
- RankComparisonGenerator
+ RankComparisonGenerator
@@ -1377,10 +1378,9 @@
Class for writing the run comparison of rank assignment for prioritisation.
-
-
- Source code in src/pheval/analyse/generate_summary_outputs.py
- 15
+
+ Source code in src/pheval/analyse/generate_summary_outputs.py
+ 15
16
17
18
@@ -1506,7 +1506,7 @@ """
self . _calculate_rank_difference () . to_csv ( prefix + suffix , sep = " \t " )
+
@@ -1520,12 +1520,13 @@
-__init__ ( run_comparison ) __init__ ( run_comparison )
@@ -1534,6 +1535,8 @@
defaultdict A nested dictionary containing the run comparison data.
+
+
A nested dictionary containing the run comparison data.
+
required
@@ -1558,9 +1565,9 @@
- Source code in src/pheval/analyse/generate_summary_outputs.py
- 18
+
+ Source code in src/pheval/analyse/generate_summary_outputs.py
+ 18
19
20
21
@@ -1576,17 +1583,18 @@ """
self . run_comparison = run_comparison
+
-generate_comparison_output ( prefix , suffix ) generate_comparison_output ( prefix , suffix )
@@ -1595,6 +1603,8 @@
str
Prefix for the output file name.
+
+
Prefix for the output file name.
+
required
@@ -1621,7 +1635,11 @@
+ Suffix for the output file name.
+
+
required
@@ -1629,9 +1647,9 @@
- Source code in src/pheval/analyse/generate_summary_outputs.py
- 69
+
+ Source code in src/pheval/analyse/generate_summary_outputs.py
+ 69
70
71
72
@@ -1649,17 +1667,18 @@ """
self . _calculate_rank_difference () . to_csv ( prefix + suffix , sep = " \t " )
+
-generate_output ( prefix , suffix ) generate_output ( prefix , suffix )
@@ -1668,6 +1687,8 @@
str
Prefix for the output file name.
+
+
Prefix for the output file name.
+
required
@@ -1694,7 +1719,11 @@
+ Suffix for the output file name.
+
+
required
@@ -1702,9 +1731,9 @@
- Source code in src/pheval/analyse/generate_summary_outputs.py
- 59
+
+ Source code in src/pheval/analyse/generate_summary_outputs.py
+ 59
60
61
62
@@ -1722,7 +1751,7 @@ """
self . _generate_dataframe () . to_csv ( prefix + suffix , sep = " \t " )
+
-generate_benchmark_comparison_output ( benchmarking_results , plot_type , benchmark_generator ) generate_benchmark_comparison_output ( benchmarking_results , plot_type , benchmark_generator )
@@ -1753,6 +1784,8 @@
List [BenchmarkRunResults ] A list containing BenchmarkRunResults instances
-representing the benchmarking results of multiple runs.
+
+
A list containing BenchmarkRunResults instances
+representing the benchmarking results of multiple runs.
+
required
@@ -1780,7 +1817,11 @@
+ The type of plot to be generated.
+
+
required
@@ -1790,7 +1831,11 @@ BenchmarkRunOutputGenerator
- Object containing benchmarking output generation details.
+
+
Object containing benchmarking output generation details.
+
required
@@ -1798,9 +1843,9 @@
- Source code in src/pheval/analyse/generate_summary_outputs.py
- 137
+
+ Source code in src/pheval/analyse/generate_summary_outputs.py
+ 137
138
139
140
@@ -1878,17 +1923,18 @@ plot_type,
)
+
-generate_benchmark_output ( benchmarking_results , plot_type , benchmark_generator ) generate_benchmark_output ( benchmarking_results , plot_type , benchmark_generator )
@@ -1897,6 +1943,8 @@
Generate prioritisation outputs for a single benchmarking run.
+
+
Parameters:
@@ -1913,7 +1961,11 @@
BenchmarkRunResults Results of a benchmarking run.
+
+
Results of a benchmarking run.
+
required
@@ -1923,7 +1975,11 @@
str
- Type of plot to generate.
+
+
Type of plot to generate.
+
required
@@ -1933,7 +1989,11 @@
BenchmarkRunOutputGenerator Object containing benchmarking output generation details.
+
+
Object containing benchmarking output generation details.
+
required
@@ -1941,9 +2001,9 @@
-
- Source code in src/pheval/analyse/generate_summary_outputs.py
- 80
+
+ Source code in src/pheval/analyse/generate_summary_outputs.py
+ 80
81
82
83
@@ -1991,17 +2051,18 @@ plot_type,
)
+
-merge_results ( result1 , result2 ) merge_results ( result1 , result2 )
@@ -2015,6 +2076,8 @@
+ The first dictionary to be merged.
+
+
required
@@ -2041,7 +2108,11 @@
+ The second dictionary to be merged.
+
+
required
@@ -2049,6 +2120,8 @@ defaultdict
- The merged dictionary containing the combined contents of result1 and result2.
+
+
The merged dictionary containing the combined contents of result1 and result2.
+
-
- Source code in src/pheval/analyse/generate_summary_outputs.py
- 106
+
+ Source code in src/pheval/analyse/generate_summary_outputs.py
+ 106
107
108
109
@@ -2127,7 +2204,7 @@ result1[ key ] = val
return result1
+
- src.pheval.analyse.parse_benchmark_summary
+ parse_benchmark_summary
- parse_benchmark_result_summary()
+ parse_benchmark_result_summary
- read_benchmark_tsv_result_summary()
+ read_benchmark_tsv_result_summary
@@ -1221,21 +1221,21 @@
- src.pheval.analyse.parse_benchmark_summary
+ parse_benchmark_summary
- parse_benchmark_result_summary()
+ parse_benchmark_result_summary
- read_benchmark_tsv_result_summary()
+ read_benchmark_tsv_result_summary
@@ -1265,6 +1265,7 @@ Parse benchmark summary
+
@@ -1280,12 +1281,13 @@
Parse benchmark summary
+
-parse_benchmark_result_summary ( benchmarking_df ) parse_benchmark_result_summary ( benchmarking_df )
@@ -1294,6 +1296,8 @@
benchmarking_df
- pd .DataFrame DataFrame
- Summary benchmark DataFrame containing columns such as
+
+
+
Summary benchmark DataFrame containing columns such as
'results_directory_path', 'top', 'top3', 'top5', 'top10',
- 'found', 'total', 'mean_reciprocal_rank'.
+ 'found', 'total', 'mean_reciprocal_rank'.
+
+
required
@@ -1320,6 +1328,8 @@
List [BenchmarkRunResults ]List[BenchmarkRunResults]: A list of BenchmarkRunResults instances generated from the DataFrame.
+
+
List[BenchmarkRunResults]: A list of BenchmarkRunResults instances generated from the DataFrame.
+
-
- Source code in src/pheval/analyse/parse_benchmark_summary.py
- 39
+
+ Source code in src/pheval/analyse/parse_benchmark_summary.py
+ 39
40
41
42
@@ -1400,17 +1414,18 @@ benchmarking_results. append ( benchmarking_result )
return benchmarking_results
+
-read_benchmark_tsv_result_summary ( benchmarking_tsv ) read_benchmark_tsv_result_summary ( benchmarking_tsv )
@@ -1419,6 +1434,8 @@
Path Path to the summary benchmark TSV output file.
+
+
Path to the summary benchmark TSV output file.
+
required
@@ -1443,6 +1464,8 @@
- pd .DataFrame DataFrame
- pd.DataFrame: A pandas DataFrame containing specific columns from the TSV file, including:
+
+
+
pd.DataFrame: A pandas DataFrame containing specific columns from the TSV file, including:
'results_directory_path', 'top', 'top3', 'top5', 'top10', 'found',
- 'total', 'mean_reciprocal_rank'.
+ 'total', 'mean_reciprocal_rank'.
+
+
-
- Source code in src/pheval/analyse/parse_benchmark_summary.py
- 11
+
+ Source code in src/pheval/analyse/parse_benchmark_summary.py
+ 11
12
13
14
@@ -1517,7 +1544,7 @@ ],
)
+
- src.pheval.analyse.parse_pheval_result
+ parse_pheval_result
- parse_pheval_result()
+ parse_pheval_result
- read_standardised_result()
+ read_standardised_result
@@ -1221,21 +1221,21 @@
- src.pheval.analyse.parse_pheval_result
+ parse_pheval_result
- parse_pheval_result()
+ parse_pheval_result
- read_standardised_result()
+ read_standardised_result
@@ -1265,6 +1265,7 @@ Parse pheval result
+
@@ -1280,12 +1281,13 @@
Parse pheval result
+
-parse_pheval_result ( data_class_type , pheval_result ) parse_pheval_result ( data_class_type , pheval_result )
@@ -1294,6 +1296,8 @@ PhEvalResult
The data class type to parse the result into.
+
+
The data class type to parse the result into.
+
required
@@ -1320,7 +1328,11 @@ List[dict]
- A list of dictionaries representing the PhEval result.
+
+
A list of dictionaries representing the PhEval result.
+
required
@@ -1328,6 +1340,8 @@ List[PhEvalResult ]
- List[PhEvalResult]: A list of instances of the specified data class type,
+
+
List[PhEvalResult]: A list of instances of the specified data class type,
+
List [PhEvalResult ]
- each instance representing a row in the PhEval result.
+
+
each instance representing a row in the PhEval result.
+
-
- Source code in src/pheval/analyse/parse_pheval_result.py
- 29
+
+ Source code in src/pheval/analyse/parse_pheval_result.py
+ 29
30
31
32
@@ -1384,17 +1406,18 @@ """
return [ data_class_type ( ** row ) for row in pheval_result ]
+
-read_standardised_result ( standardised_result_path ) read_standardised_result ( standardised_result_path )
@@ -1403,6 +1426,8 @@ Path
The path to the file containing the standardised result output.
+
+
The path to the file containing the standardised result output.
+
required
@@ -1427,6 +1456,8 @@ List[dict]
- List[dict]: A list of dictionaries representing the content of the standardised result file.
+
+
List[dict]: A list of dictionaries representing the content of the standardised result file.
+
-
- Source code in src/pheval/analyse/parse_pheval_result.py
- 12
+
+ Source code in src/pheval/analyse/parse_pheval_result.py
+