Save changes to fix labeling

meyer-lab · Nov 5, 2024 · 73801ef · 73801ef
1 parent 527409e
commit 73801ef
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Showing 5 changed files with 18 additions and 11 deletions.
diff --git a/pf2/figures/commonFuncs/plotGeneral.py b/pf2/figures/commonFuncs/plotGeneral.py
@@ -93,7 +93,7 @@ def add_obs_cmp_both_label(
             else:
                 thres_value = top_perc
                 threshold2 = np.percentile(wprojs, thres_value, axis=0)
-                idx = wprojs[:, cmp - 1] < threshold1[cmp - 1]
+                idx = wprojs[:, cmp - 1] < threshold2[cmp - 1]
 
         X.obs[f"Cmp{cmp}"] = idx
 

diff --git a/pf2/figures/figureA11.py b/pf2/figures/figureA11.py
@@ -24,8 +24,8 @@ def makeFigure():
     add_obs(X, "patient_category")
     combine_cell_types(X)
 
-    cmp1 = 27; cmp2 = 46
-    pos1 = True; pos2 = True
+    cmp1 = 2; cmp2 = 25
+    pos1 = True; pos2 = False
     threshold = 0.5
     X = add_obs_cmp_both_label(X, cmp1, cmp2, pos1, pos2, top_perc=threshold)
     X = add_obs_label(X, cmp1, cmp2)

diff --git a/pf2/figures/figureA14.py b/pf2/figures/figureA14.py
@@ -8,6 +8,7 @@
 from ..figures.commonFuncs.plotGeneral import add_obs_cmp_both_label, add_obs_label
 import seaborn as sns
 import matplotlib.colors as mcolors
+import numpy as np
 
 def makeFigure():
     """Get a list of the axis objects and create a figure."""
@@ -20,17 +21,23 @@ def makeFigure():
     add_obs(X, "patient_category")
     combine_cell_types(X)
 
-    cmp1 = 27; cmp2 = 46
-    pos1 = True; pos2 = True
+    cmp1 = 2; cmp2 = 25
+    pos1 = True; pos2 = False
     threshold = 0.5
     X = add_obs_cmp_both_label(X, cmp1, cmp2, pos1, pos2, top_perc=threshold)
+    print(np.count_nonzero(X.obs["Cmp2"]))
+    print(np.count_nonzero(X.obs["Cmp25"]))
+    print(np.count_nonzero(X.obs["Both"]))
+
     X = add_obs_label(X, cmp1, cmp2)
+    print(np.unique(X.obs["Label"], return_counts=True))
 
     colors = ["black", "fuchsia", "turquoise", "gainsboro"]
     pal = []
     for i in colors:
         pal.append(mcolors.CSS4_COLORS[i])
 
+    print(np.unique(X.obs["Label"], return_counts=True))
     plot_labels_pacmap(X, "Label", ax[0], color_key=pal)
 
 

diff --git a/pf2/figures/figureA2.py b/pf2/figures/figureA2.py
@@ -11,8 +11,8 @@ def makeFigure():
 
     X = read_h5ad("/opt/northwest_bal/full_fitted.h5ad", backed="r")
 
-    for i in [24, 25, 49]:
-        plot_wp_pacmap(X, i, ax[i - 1], cbarMax=0.4)
-        # plot_wp_per_celltype(X, i, ax[i-1])
+    for i, cmp in enumerate([2, 25, 19, 26, 34, 27, 37, 44, 8, 31]):
+        plot_wp_pacmap(X, cmp, ax[2*i], cbarMax=0.4)
+        plot_wp_per_celltype(X, cmp, ax[2*i + 1])
 
     return f
diff --git a/pf2/figures/figureA7.py b/pf2/figures/figureA7.py
@@ -17,7 +17,7 @@
 
 def makeFigure():
     """Get a list of the axis objects and create a figure."""
-    ax, f = getSetup((10, 10), (2, 2))
+    ax, f = getSetup((15, 15), (4, 4))
 
     X = anndata.read_h5ad("/opt/northwest_bal/full_fitted.h5ad")
     X = add_obs(X, "binary_outcome")
@@ -26,9 +26,9 @@ def makeFigure():
 
     celltype_count_perc_df = cell_count_perc_df(X, celltype="cell_type")
 
-    for i in range(4):
+    for i, cmp in enumerate([2, 25, 19, 26, 34, 27, 37, 44, 8, 31]):
         plot_correlation_cmp_cell_count_perc(
-            X, i + 1, celltype_count_perc_df, ax[i], cellPerc=True
+            X, cmp, celltype_count_perc_df, ax[i], cellPerc=True
         )
 
     return f