PaCMAP figures

spatialpf2/figures/figureSpatial1.py

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+"""
+PaCMAP of Weighted Projections based on Pf2
+"""
+
+from ..imports import import_HTAN
+from .common import subplotLabel, getSetup
+from .commonFuncs.plotPaCMAP import plot_wp_pacmap
+from ..factorization import pf2
+
+
+def makeFigure():
+    ax, f = getSetup((12, 10), (5, 4))
+    subplotLabel(ax)
+
+    X = import_HTAN()
+
+    rank = 20
+    X = pf2(X, rank, doEmbedding=True)
+
+    for i in range(1, 21):
+        plot_wp_pacmap(X, i, ax[i - 1], cbarMax=0.25)
+
+    return f

spatialpf2/figures/figureSpatial2.py

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+"""
+PaCMAP of immune exclusion signature genes
+"""
+from ..imports import import_HTAN
+from .common import subplotLabel, getSetup
+from .commonFuncs.plotPaCMAP import plot_gene_pacmap
+from ..factorization import pf2
+
+def makeFigure():
+    ax, f = getSetup((15, 8), (2, 4))
+
+    subplotLabel(ax)
+
+    X = import_HTAN()
+
+    rank = 20
+    X = pf2(X, rank, doEmbedding=True)
+
+    # genes originate from epithelial cells
+    plot_gene_pacmap("DDR1", "Pf2", X, ax[0])
+    plot_gene_pacmap("TGFBI", "Pf2",  X, ax[1])
+    plot_gene_pacmap("PAK4", "Pf2",  X, ax[2])
+    plot_gene_pacmap("DPEP1", "Pf2",  X, ax[3])
+
+
+
+
+
+    return f    

spatialpf2/figures/figureSpatial3.py

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+"""
+PaCMAP of Conditions
+"""
+
+from ..imports import import_HTAN
+from .common import subplotLabel, getSetup
+import numpy as np
+from .commonFuncs.plotPaCMAP import plot_labels_pacmap
+from ..factorization import pf2
+
+def makeFigure():
+    ax, f = getSetup((8, 8), (1, 1))
+
+    subplotLabel(ax)
+
+    X = import_HTAN()
+
+    rank = 20
+    X = pf2(X, rank, doEmbedding=True)
+
+    plot_labels_pacmap(X, "Condition", ax[0])
+
+
+    return f