Added Figure 4

pf2barcode/figures/figure2.py

@@ -0,0 +1,11 @@
+import scanpy as sc
+from pf2barcode.imports import import_CCLE
+import seaborn as sns
+
+def makeFigure(): 
+    X = import_CCLE()
+
+    Xsel = X[:, X.var.index.str.contains('AXL')]
+    Xsel.uns
+
+    sc.pl.pca(X, color="SW", components=['1,2', '3,4'], size=10)

pf2barcode/figures/figure4.py

@@ -0,0 +1,36 @@
+import seaborn as sns
+import numpy as np
+from scipy.stats import kruskal
+import matplotlib.pyplot as plt
+
+from pf2barcode.imports import import_CCLE
+
+from .common import (
+    getSetup,
+    subplotLabel,
+)                                        
+
+def makeFigure():
+
+    X = import_CCLE()
+
+    """Get a list of the axis objects and create a figure."""
+    ax, f = getSetup((10, 6), (1, 1))
+    subplotLabel(ax)
+
+    idx_selected = 0
+    cells = []
+    pvalues = np.zeros(X.obsm["X_pca"].shape[1])
+
+    for jj in range(X.obsm["X_pca"].shape[1]):
+        for barcodes in X.obs["SW"].unique():
+            cells_selected = X.obsm["X_pca"][X.obs["SW"] == barcodes, idx_selected]
+            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

requirements-dev.lock

@@ -61,6 +61,8 @@ idna==3.8
     # via requests
 igraph==0.11.6
     # via pf2barcode
+importlib-metadata==8.5.0
+    # via dask
 iniconfig==2.0.0
     # via pytest
 ipykernel==6.29.5
@@ -252,6 +254,7 @@ traitlets==5.14.3
     # via jupyter-core
     # via matplotlib-inline
 typing-extensions==4.12.2
+    # via ipython
     # via pyright
 tzdata==2024.1
     # via pandas
@@ -263,3 +266,5 @@ wcwidth==0.2.13
     # via prompt-toolkit
 widgetsnbextension==4.0.13
     # via ipywidgets
+zipp==3.20.2
+    # via importlib-metadata

requirements.lock

@@ -59,6 +59,8 @@ idna==3.8
     # via requests
 igraph==0.11.6
     # via pf2barcode
+importlib-metadata==8.5.0
+    # via dask
 ipykernel==6.29.5
     # via pf2barcode
 ipython==8.27.0
@@ -238,6 +240,8 @@ traitlets==5.14.3
     # via jupyter-client
     # via jupyter-core
     # via matplotlib-inline
+typing-extensions==4.12.2
+    # via ipython
 tzdata==2024.1
     # via pandas
 umap-learn==0.5.6
@@ -248,3 +252,5 @@ wcwidth==0.2.13
     # via prompt-toolkit
 widgetsnbextension==4.0.13
     # via ipywidgets
+zipp==3.20.2
+    # via importlib-metadata