scRNA-seq_analysis

tools/force_abstract_graph_2D/make_fdg.py

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+import sys
+args = sys.argv
+n_iterations = int(args[1])
+pca_data_fname = args[2]
+snn_fname = args[3]
+fdg_coordinates_fname = args[4]
+
+from fa2 import ForceAtlas2
+import pandas as pd
+from scipy.io import mmread
+import numpy as np
+
+# load pca, SNN and label colours data
+# the first 2 PC form PCA are used as initial conditions
+# SNN is used for building the force directed graph
+pca_data = pd.read_csv(pca_data_fname, index_col = 0)
+snn      = mmread(snn_fname)
+
+# set initialposition as the first 2 PCs
+positions = pca_data.values[:, 0:2]
+
+# initialize force directed graph class instance
+forceatlas2 = ForceAtlas2(outboundAttractionDistribution=False, linLogMode=False,
+                          adjustSizes=False, edgeWeightInfluence=1.0,
+                          jitterTolerance=1.0, barnesHutTheta = .8,
+                          barnesHutOptimize=True, multiThreaded=False,
+                          scalingRatio=2.0, strongGravityMode=True, gravity=1, verbose=True)
+
+# run force directed graph; for each iterations generates the coordinates use din each frame
+coord = forceatlas2.forceatlas2(G = snn, pos = positions, iterations = n_iterations)
+coord = np.array(coord)
+
+np.savetxt( fname = fdg_coordinates_fname, X = coord, delimiter = ",")