adding buffer for 0 division

Author: nbedanova

pf2rnaseq/figures/commonFuncs/plotFactors.py

@@ -18,21 +18,19 @@ def plot_condition_factors(
     cond_group_labels: pd.Series | None = None,
     groupConditions=False,
     cond="Condition",
-    log_scale=True,
-    centering=True
+    log_scale=True
 ):
     """Plots Pf2 condition factors"""
     pd.set_option("display.max_rows", None)
     yt = pd.Series(np.unique(data.obs[cond]))
     X = np.array(data.uns["Pf2_A"])
     if log_scale:
         X = np.log10(X)
-    if centering:
-        X -= np.median(X, axis=0)
-        X /= np.std(X, axis=0)
-        ind = reorder_table(X)
-    else:
-        ind = np.arange(len(X))
+    
+    X -= np.median(X, axis=0)
+    X /= np.std(X, axis=0)+1e-3
+    ind = reorder_table(X+1e-3)
+
     X = X[ind]
     yt = yt.iloc[ind]
 

pf2rnaseq/figures/figureParseFactorsDeconv.py

@@ -35,7 +35,7 @@ def makeFigure():
     X = read_h5ad("/home/nicoleb/ParsePf2_100_D11_filt.h5ad")
     X.uns["Pf2_A"] = correct_conditions(X)
 
-    W, H = deconvolution_cytokine(X.uns["Pf2_A"], alpha=9e-5, max_iter=5000)
+    W, H = deconvolution_cytokine(X.uns["Pf2_A"], alpha=1e-1, max_iter=5000)
 
 
     # Get cytokine names in correct order
@@ -51,8 +51,7 @@ def makeFigure():
         samples_df["cytokine"],
         groupConditions=True,
         cond="cytokine",
-        log_scale=False,
-        centering=False
+        log_scale=False
     )
     ax[0].set_title("Deconvolved matrix (H)", fontsize=12, fontweight="bold")
 
@@ -62,8 +61,7 @@ def makeFigure():
         samples_df["cytokine"],
         groupConditions=True,
         cond="cytokine",
-        log_scale=False,
-        centering=False
+        log_scale=False
     )
     ax[1].set_title("Original Effects (A)", fontsize=12, fontweight="bold")