geney 1.2.47__py2.py3-none-any.whl → 1.2.49__py2.py3-none-any.whl

geney/survival_utils.py

@@ -64,7 +64,7 @@ class SurvivalAnalysis:
                                  df[col].nunique() > 1]]  # and df[col].value_counts(normalize=True).min() >= 0.01]]
         return df
 
-    def kaplan_meier_analysis(self, df, control_label='CV', target_label='Epistasis', feature='group', plot=False, time_cap=False, ax=None):
+    def kaplan_meier_analysis(self, df, control_label='Unaffected Patients', target_label='Affected Patients', feature='group', plot=False, title=None, time_cap=False, savepath=None, figsize=(7, 3), tmb_p_value=None):
         # Can only be performed on features with two unique values
         cap_time = df.groupby(feature).duration.max().min()
         # df['duration'] = df['duration'].clip(upper=cap_time)
@@ -88,6 +88,7 @@ class SurvivalAnalysis:
             auc_vals.append(auc)
             if plot:
                 if count == 0:
+                    fig, ax = plt.subplots(figsize=figsize)
                     kmf.plot_survival_function(ax=ax, ci_show=True, color="#2430e0", lw=2)
                 else:
                     kmf.plot_survival_function(ax=ax, ci_show=True, color="#e60215", lw=2)
@@ -96,14 +97,19 @@ class SurvivalAnalysis:
         p_value = self.log_rank(df[df[feature] == 1], df[df[feature] == 0])
 
         if plot:
-            ax.text(0.5, 0.85, rf'Survival $p{{v}}$: {p_value:.3e}', transform=ax.transAxes, fontsize=10,
+            ax.text(0.82, 0.6, rf'Survival $p{{v}}$: {p_value:.3e}', transform=ax.transAxes, fontsize=10,
                     horizontalalignment='center')
+            if tmb_p_value:
+                ax.text(0.82, 0.53, rf'TMB $p{{v}}$: {tmb_p_value:.3e}', transform=ax.transAxes, fontsize=10,
+                        horizontalalignment='center')
             # Grid and spines
             ax.grid(True, which="major", linestyle="--", linewidth=0.5, color="grey", alpha=0.7)
             ax.spines['top'].set_visible(False)
             ax.spines['right'].set_visible(False)
             ax.tick_params(axis="both", which="major", labelsize=10)
-            legend = ax.legend(fontsize=12, loc='upper right', frameon=True)
+            if title:
+                ax.set_title(title, fontsize=12)
+            legend = ax.legend(fontsize=9, loc='upper right', frameon=True)
             legend.get_frame().set_facecolor('white')  # Set the background color to white
             legend.get_frame().set_edgecolor('black')  # Set the edge color to black
             plt.xlabel('Time (years)')
@@ -111,8 +117,9 @@ class SurvivalAnalysis:
             if time_cap:
                 plt.xlim([0, cap_time])
             plt.tight_layout()
-
-            # plt.show()
+            if savepath is not None:
+                plt.savefig(savepath, bbox_inches='tight', dpi=300)
+            plt.show()
 
         results['p_value'] = p_value
         results['auc_target'] = auc_vals[-1]

{geney-1.2.47.dist-info → geney-1.2.49.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: geney
-Version: 1.2.47
+Version: 1.2.49
 Summary: A Python package for gene expression modeling.
 Home-page: https://github.com/nicolaslynn/geney
 Author: Nicolas Lynn

{geney-1.2.47.dist-info → geney-1.2.49.dist-info}/RECORD

@@ -12,7 +12,7 @@ geney/power_utils.py,sha256=MehZFUdkJ2EFUot709yPEDxSkXmH5XevMebX2HD768A,7330
 geney/seqmat_utils.py,sha256=YV5DFLbfjXLIswPGvqK1-eEfwn9TUby0b2kewdGAKws,18372
 geney/spliceai_utils.py,sha256=gIGPC8u3J15A7EQrk2Elho5PbF9MmUUNopGGH-eEV8s,1873
 geney/splicing_utils.py,sha256=lGBNknnAdKhcJ3MqPQ5c9oz_NKcL2lcFAr78StjKa6o,16151
-geney/survival_utils.py,sha256=S66tKOMwGSSFXb-2MYg8ZEuyDV64942VB4eFcXRFQas,6392
+geney/survival_utils.py,sha256=5DkV4HuXdFIfbVshRhdCFa59QD6DWAwLjjt98oBfGZ8,6893
 geney/tcga_utils.py,sha256=D_BNHm-D_K408dlcJm3hzH2c6QNFjQsKvUcOPiQRk7g,17612
 geney/tis_utils.py,sha256=vA2ci4gNfwwQZlCjPpO5ehvL2NRVeM7lHI_VyfT-_10,8049
 geney/utils.py,sha256=EsKvBM-Nz2a3_4ZAhF4Dxd4PwT7_6YYKpxEN4LLgg10,2174
@@ -20,7 +20,7 @@ geney/translation_initiation/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NM
 geney/translation_initiation/tis_utils.py,sha256=AF3siFjuQH-Rs44EV-80zHdbxRMvN4woLFSHroWIETc,4448
 geney/translation_initiation/resources/kozak_pssm.json,sha256=pcd0Olziutq-6H3mFWDCD9cujQ_AlZO-iiOvBl82hqE,1165
 geney/translation_initiation/resources/tis_regressor_model.joblib,sha256=IXb4DUDhJ5rBDKcqMk9zE3ECTZZcdj7Jixz3KpoZ7OA,2592025
-geney-1.2.47.dist-info/METADATA,sha256=fdtNRwV6GwITCTn1O3J0ytlq1wNYda0_sGJdMiNuZU4,948
-geney-1.2.47.dist-info/WHEEL,sha256=fS9sRbCBHs7VFcwJLnLXN1MZRR0_TVTxvXKzOnaSFs8,110
-geney-1.2.47.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
-geney-1.2.47.dist-info/RECORD,,
+geney-1.2.49.dist-info/METADATA,sha256=lKeYqaJwqQigXx3rmxyumCqWx7Y2j2H7gq5OsCeUFuM,948
+geney-1.2.49.dist-info/WHEEL,sha256=fS9sRbCBHs7VFcwJLnLXN1MZRR0_TVTxvXKzOnaSFs8,110
+geney-1.2.49.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
+geney-1.2.49.dist-info/RECORD,,