diff --git a/tspex/core/auxiliary_functions.py b/tspex/core/auxiliary_functions.py index 9938936..68fd417 100644 --- a/tspex/core/auxiliary_functions.py +++ b/tspex/core/auxiliary_functions.py @@ -46,8 +46,7 @@ def dpm(vector): """ n = len(vector) - dispersion_measure = np.std(vector, ddof=1) * np.sqrt(n) - return dispersion_measure + return np.std(vector, ddof=1) * np.sqrt(n) def tukey_biweight(vector, c=5, epsilon=1e-4): @@ -76,8 +75,7 @@ def tukey_biweight(vector, c=5, epsilon=1e-4): i = np.abs(u) > 1 w = (1 - u ** 2) ** 2 w[i] = 0 - tbi = np.sum(w * vector) / np.sum(w) - return tbi + return np.sum(w * vector) / np.sum(w) def entropy(vector): @@ -106,8 +104,7 @@ def entropy(vector): else: p = vector / np.sum(vector) p = p[np.nonzero(p)[0]] - h = -1 * np.dot(p, np.log2(p)) - return h + return -1 * np.dot(p, np.log2(p)) def roku(vector): @@ -136,8 +133,7 @@ def roku(vector): tbi = tukey_biweight(vector) vector_p = np.abs(vector - tbi) - h = entropy(vector_p) - return h + return entropy(vector_p) def js_distance(p, q): @@ -168,5 +164,4 @@ def js_distance(p, q): left = entropy((p + q) / 2) right = (entropy(p) + entropy(q)) / 2 js = left - right - jsd = np.sqrt(js) - return jsd + return np.sqrt(js) diff --git a/tspex/core/specificity_functions.py b/tspex/core/specificity_functions.py index e5e1f85..a455ea6 100644 --- a/tspex/core/specificity_functions.py +++ b/tspex/core/specificity_functions.py @@ -78,8 +78,7 @@ def counts(vector, **kwargs): if cts == 0: return 0.0 else: - cts_transformed = (1 - (cts / n)) * (n / (n - 1)) - return cts_transformed + return (1 - (cts / n)) * (n / (n - 1)) def tau(vector, **kwargs): @@ -110,8 +109,7 @@ def tau(vector, **kwargs): else: n = len(vector) vector_r = vector / np.max(vector) - tau_index = np.sum(1 - vector_r) / (n - 1) - return tau_index + return np.sum(1 - vector_r) / (n - 1) def gini(vector, **kwargs): @@ -149,8 +147,7 @@ def gini(vector, **kwargs): index = np.arange(1, n + 1) gini_coefficient = (np.sum((2 * index - n - 1) * vector)) / (n * np.sum(vector)) if transform: - transformed_gini_coefficient = gini_coefficient * (n / (n - 1)) - return transformed_gini_coefficient + return gini_coefficient * (n / (n - 1)) else: return gini_coefficient @@ -187,8 +184,7 @@ def simpson(vector, **kwargs): simpson_index = np.sum(p ** 2) if transform: min_simpson = 1 / len(vector) - transformed_simpson_index = (simpson_index - min_simpson) / (1 - min_simpson) - return transformed_simpson_index + return (simpson_index - min_simpson) / (1 - min_simpson) else: return simpson_index @@ -227,8 +223,7 @@ def shannon_specificity(vector, **kwargs): n = len(vector) ss = np.log2(n) - entropy(vector) if transform: - ss_transformed = ss / np.log2(n) - return ss_transformed + return ss / np.log2(n) else: return ss @@ -271,8 +266,7 @@ def roku_specificity(vector, **kwargs): n = len(vector) rs = np.log2(n) - roku(vector) if transform: - rs_transformed = rs / np.log2(n) - return rs_transformed + return rs / np.log2(n) else: return rs @@ -303,8 +297,7 @@ def tsi(vector, **kwargs): if not np.any(vector): return 0.0 else: - tissue_specificity_index = vector / np.sum(vector) - return tissue_specificity_index + return vector / np.sum(vector) def zscore(vector, **kwargs): @@ -342,8 +335,7 @@ def zscore(vector, **kwargs): zs = (vector - np.mean(vector)) / std if transform: max_zs = (n - 1) / np.sqrt(n) - zs_transformed = (zs + max_zs) / (2 * max_zs) - return zs_transformed + return (zs + max_zs) / (2 * max_zs) else: return zs @@ -407,8 +399,7 @@ def spm_dpm(vector, **kwargs): """ spm_vector = spm(vector) - spm_dispersion = dpm(spm_vector) - return spm_dispersion + return dpm(spm_vector) def js_specificity(vector, **kwargs): @@ -475,5 +466,4 @@ def js_specificity_dpm(vector, **kwargs): """ js_vector = js_specificity(vector) - js_specificity_dispersion = dpm(js_vector) - return js_specificity_dispersion + return dpm(js_vector)