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meyer-lab · Sep 3, 2024 · a9b00cc · a9b00cc
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Showing 7 changed files with 213 additions and 175 deletions.
diff --git a/pf2/figures/figureA10.py b/pf2/figures/figureA10.py
@@ -28,9 +28,9 @@ def makeFigure():
     #         ), ax[0], percentList=percentList, runs=3)
 
     print(X)
-    ranks = list([5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70])
+    ranks = list([10, 20, 30, 40, 50, 60, 70])
     XX = sc.pp.subsample(
-                X, fraction=.02, copy=True, random_state=1
+                X, fraction=.1, copy=True, random_state=1
             )
     print(XX)
     plot_fms_diff_ranks(XX, ax[1], ranksList=ranks, runs=3)
@@ -85,6 +85,7 @@ def plot_fms_percent_drop(
 
             fmsScore = calculateFMS(dataX, sampledX)
             scores.append(fmsScore)
+            print(i)
 
         fmsLists.append(scores)
 

diff --git a/pf2/figures/figureA11.py b/pf2/figures/figureA11.py
@@ -37,8 +37,15 @@ def makeFigure():
     X.obs["Label"] = df["Cell Type"].astype(str) + df["Label"].astype(str)
 
     print(X)
-    # sc.tl.rank_genes_groups(X, "Label", method="wilcoxon", groups=["MacrophagesCmp3", "MacrophagesCmp26"], reference="MacrophagesNoLabel")
-    # sc.pl.rank_genes_groups(X, n_genes=30, save="Cmp_3_26.png")
+
+    XX = X[(X.obs["Label"] == "MacrophagesCmp3") & (X.obs["Label"] == "MacrophagesCmp26") & (X.obs["Label"] == "MacrophagesNoLabel")]
+
+    sc.tl.rank_genes_groups(X, "Label", method="wilcoxon", groups="MacrophagesCmp3", reference="MacrophagesCmp26")
+    sc.pl.rank_genes_groups(X, n_genes=30, save="Cmp_3_26_wilcoxon.png")
+
+
+    # sc.tl.rank_genes_groups(X, "Label", method="'t-test", groups=["MacrophagesCmp3", "MacrophagesCmp26"], reference="MacrophagesNoLabel")
+    # sc.pl.rank_genes_groups(X, n_genes=30, save="Cmp_3_26_test.png")
 
     return f
 

diff --git a/pf2/figures/figureA13.py b/pf2/figures/figureA13.py
@@ -25,8 +25,8 @@ def makeFigure():
     add_obs(X, "patient_category")
     combine_cell_types(X)
 
-    cmp1 = 3
-    cmp2 = 26
+    cmp1 = 1
+    cmp2 = 13
     threshold = .5
     X = add_cmp_both_label(X, cmp1, cmp2, pos1=False, pos2=False, top_perc=threshold)
 
@@ -35,7 +35,7 @@ def makeFigure():
 
     # genes = np.concatenate([genes1, genes2])
 
-    genes = ["KIF20A", "NEK2", "FAM111B", "RAD54L"]
+    genes = ["PADI4", "EDN1", "CRYAB", "C11orf96"]
     for i, gene in enumerate(genes):
         plot_avegene_per_cmp(X, gene, ax[i], cmp1, cmp2, both_cmp = False, cell_type=True)
         rotate_xaxis(ax[i])

diff --git a/pf2/figures/figureA2.py b/pf2/figures/figureA2.py
@@ -14,18 +14,18 @@ def makeFigure():
 
     X = read_h5ad("/opt/northwest_bal/full_fitted.h5ad", backed="r")
 
-    cmp1 = 3
-    cmp2 = 26
+    cmp1 = 1
+    cmp2 = 13
     threshold = .5
-    X = add_cmp_both_label(X, cmp1, cmp2, pos1=True, pos2=True, top_perc=threshold)
+    X = add_cmp_both_label(X, cmp1, cmp2, pos1=False, pos2=False, top_perc=threshold)
 
 
 
-    X_cmp1 = X[(X.obs[f"Cmp{cmp1}"] == True)]
-    X_cmp2 = X[(X.obs[f"Cmp{cmp2}"] == True)]
+    # X_cmp1 = X[(X.obs[f"Cmp{cmp1}"] == True)]
+    # X_cmp2 = X[(X.obs[f"Cmp{cmp2}"] == True)]
     # for i in range(1, 51):
-    plot_wp_pacmap(X_cmp1, cmp1, ax[0], cbarMax=0.3)
-    plot_wp_pacmap(X_cmp2, cmp2, ax[1], cbarMax=0.3)
+    plot_wp_pacmap(X, cmp1, ax[0], cbarMax=0.3)
+    plot_wp_pacmap(X, cmp2, ax[1], cbarMax=0.3)
         # plot_wp_per_celltype(X, i, ax[i-1])
 
     return f

diff --git a/pf2/figures/figureA8.py b/pf2/figures/figureA8.py
@@ -46,8 +46,8 @@ def makeFigure():
 
     # for i in range(6):
     # for i in range(1):
-    cmp1 = pc_abs_df.iloc[-(3+1), 0]
-    cmp2 = pc_abs_df.iloc[-(3+1), 1]
+    cmp1 = pc_abs_df.iloc[-(3+2), 0]
+    cmp2 = pc_abs_df.iloc[-(3+2), 1]
     plot_pair_gene_factors(X, cmp1, cmp2, ax[(3*3)])
     plot_pair_cond_factors(cond_fact_meta_df, cmp1, cmp2, ax[(3*3)+1], "Status")
     # plot_pair_wp(X, cmp1, cmp2, ax[(3*3)+2], frac=.001)