diff options
Diffstat (limited to 'gn3/heatmaps.py')
| -rw-r--r-- | gn3/heatmaps.py | 62 |
1 files changed, 31 insertions, 31 deletions
diff --git a/gn3/heatmaps.py b/gn3/heatmaps.py index 45d0c22..b6fc6d3 100644 --- a/gn3/heatmaps.py +++ b/gn3/heatmaps.py @@ -27,10 +27,10 @@ from gn3.computations.qtlreaper import ( organise_reaper_main_results) def export_trait_data( - trait_data: dict, strainlist: Sequence[str], dtype: str = "val", + trait_data: dict, samplelist: Sequence[str], dtype: str = "val", var_exists: bool = False, n_exists: bool = False): """ - Export data according to `strainlist`. Mostly used in calculating + Export data according to `samplelist`. Mostly used in calculating correlations. DESCRIPTION: @@ -40,8 +40,8 @@ def export_trait_data( PARAMETERS trait: (dict) The dictionary of key-value pairs representing a trait - strainlist: (list) - A list of strain names + samplelist: (list) + A list of sample names dtype: (str) ... verify what this is ... var_exists: (bool) @@ -49,18 +49,18 @@ def export_trait_data( n_exists: (bool) A flag indicating existence of ndata """ - def __export_all_types(tdata, strain): + def __export_all_types(tdata, sample): sample_data = [] - if tdata[strain]["value"]: - sample_data.append(tdata[strain]["value"]) + if tdata[sample]["value"]: + sample_data.append(tdata[sample]["value"]) if var_exists: - if tdata[strain]["variance"]: - sample_data.append(tdata[strain]["variance"]) + if tdata[sample]["variance"]: + sample_data.append(tdata[sample]["variance"]) else: sample_data.append(None) if n_exists: - if tdata[strain]["ndata"]: - sample_data.append(tdata[strain]["ndata"]) + if tdata[sample]["ndata"]: + sample_data.append(tdata[sample]["ndata"]) else: sample_data.append(None) else: @@ -73,17 +73,17 @@ def export_trait_data( return tuple(sample_data) - def __exporter(accumulator, strain): + def __exporter(accumulator, sample): # pylint: disable=[R0911] - if strain in trait_data["data"]: + if sample in trait_data["data"]: if dtype == "val": - return accumulator + (trait_data["data"][strain]["value"], ) + return accumulator + (trait_data["data"][sample]["value"], ) if dtype == "var": - return accumulator + (trait_data["data"][strain]["variance"], ) + return accumulator + (trait_data["data"][sample]["variance"], ) if dtype == "N": - return accumulator + (trait_data["data"][strain]["ndata"], ) + return accumulator + (trait_data["data"][sample]["ndata"], ) if dtype == "all": - return accumulator + __export_all_types(trait_data["data"], strain) + return accumulator + __export_all_types(trait_data["data"], sample) raise KeyError("Type `%s` is incorrect" % dtype) if var_exists and n_exists: return accumulator + (None, None, None) @@ -91,7 +91,7 @@ def export_trait_data( return accumulator + (None, None) return accumulator + (None,) - return reduce(__exporter, strainlist, tuple()) + return reduce(__exporter, samplelist, tuple()) def trait_display_name(trait: Dict): """ @@ -165,19 +165,19 @@ def build_heatmap(traits_names, conn: Any): for fullname in traits_names] traits_data_list = [retrieve_trait_data(t, conn) for t in traits] genotype_filename = build_genotype_file(traits[0]["riset"]) - strains = load_genotype_samples(genotype_filename) + samples = load_genotype_samples(genotype_filename) exported_traits_data_list = [ - export_trait_data(td, strains) for td in traits_data_list] + export_trait_data(td, samples) for td in traits_data_list] clustered = cluster_traits(exported_traits_data_list) slinked = slink(clustered) traits_order = compute_traits_order(slinked) - strains_and_values = retrieve_strains_and_values( - traits_order, strains, exported_traits_data_list) + samples_and_values = retrieve_samples_and_values( + traits_order, samples, exported_traits_data_list) traits_filename = "{}/traits_test_file_{}.txt".format( TMPDIR, random_string(10)) generate_traits_file( - strains_and_values[0][1], - [t[2] for t in strains_and_values], + samples_and_values[0][1], + [t[2] for t in samples_and_values], traits_filename) main_output, _permutations_output = run_reaper( @@ -229,9 +229,9 @@ def compute_traits_order(slink_data, neworder: tuple = tuple()): return __order_maker(neworder, slink_data) -def retrieve_strains_and_values(orders, strainlist, traits_data_list): +def retrieve_samples_and_values(orders, samplelist, traits_data_list): """ - Get the strains and their corresponding values from `strainlist` and + Get the samples and their corresponding values from `samplelist` and `traits_data_list`. This migrates the code in @@ -240,17 +240,17 @@ def retrieve_strains_and_values(orders, strainlist, traits_data_list): # This feels nasty! There's a lot of mutation of values here, that might # indicate something untoward in the design of this function and its # dependents ==> Review - strains = [] + samples = [] values = [] rets = [] for order in orders: temp_val = traits_data_list[order] - for i, strain in enumerate(strainlist): + for i, sample in enumerate(samplelist): if temp_val[i] is not None: - strains.append(strain) + samples.append(sample) values.append(temp_val[i]) - rets.append([order, strains[:], values[:]]) - strains = [] + rets.append([order, samples[:], values[:]]) + samples = [] values = [] return rets |