Merge branch 'main' into newer_branch

pf2barcode/figures/figure4.py

@@ -0,0 +1,34 @@
+import matplotlib.pyplot as plt
+import numpy as np
+import seaborn as sns
+from scipy.stats import kruskal
+
+from pf2barcode.imports import import_CCLE
+
+from .common import (
+    getSetup,
+    subplotLabel,
+)
+
+
+def makeFigure():
+    X = import_CCLE()
+
+    ax, f = getSetup((10, 6), (1, 1))
+    subplotLabel(ax)
+
+    pvalues = np.zeros(X.obsm["X_pca"].shape[1])
+
+    for jj in range(X.obsm["X_pca"].shape[1]):
+        cells = []
+        for barcodes in X.obs["SW"].unique():
+            cells_selected = X.obsm["X_pca"][X.obs["SW"] == barcodes, jj]
+            cells.append(cells_selected.flatten())
+
+        pvalues[jj] = kruskal(*cells).pvalue
+
+    sns.barplot(x=np.arange(pvalues.shape[0]), y=-np.log10(pvalues))
+    plt.xlabel("PC")
+    plt.ylabel("-log10(p-value)")
+
+    return f