From 649e08a09d85f986e75bb67e5c14959ad59c6f27 Mon Sep 17 00:00:00 2001
From: Constantin Pape <constantin.pape@iwr.uni-heidelberg.de>
Date: Thu, 7 Nov 2019 15:39:36 +0100
Subject: [PATCH] Implement preliminary cilia analysis
---
analysis/cilia/analyse_cilia.py | 88 +++++++++++++++++++++++++++++++++
1 file changed, 88 insertions(+)
create mode 100644 analysis/cilia/analyse_cilia.py
diff --git a/analysis/cilia/analyse_cilia.py b/analysis/cilia/analyse_cilia.py
new file mode 100644
index 0000000..4ee31cd
--- /dev/null
+++ b/analysis/cilia/analyse_cilia.py
@@ -0,0 +1,88 @@
+import numpy as np
+import pandas as pd
+from make_cell_table import right_nephr_ids, left_nephr_ids
+from matplotlib import pyplot as plt
+
+TABLE_PATH = '../../data/0.6.2/tables/sbem-6dpf-1-whole-segmented-cilia-labels/cell_mapping.csv'
+
+
+def check_cell_ids():
+ table = pd.read_csv(TABLE_PATH, sep='\t')
+ cell_ids = table['cell_id'].values
+
+ matched_right = []
+ matched_left = []
+ for cell_id in cell_ids:
+ if cell_id in right_nephr_ids:
+ matched_right.append(cell_id)
+ elif cell_id in left_nephr_ids:
+ matched_left.append(cell_id)
+ else:
+ assert cell_id == 0 or np.isnan(cell_id), str(cell_id)
+
+ matched_right = set(matched_right)
+ matched_left = set(matched_left)
+
+ # unmatched_right = set(right_nephr_ids) - matched_right
+ # unmatched_left = set(left_nephr_ids) - matched_left
+
+ print("Number of cells right:")
+ print("Total:", len(right_nephr_ids))
+ print("With cilia:", len(matched_right))
+
+ print("Number of cells left:")
+ print("Total:", len(left_nephr_ids))
+ print("With cilia:", len(matched_left))
+
+
+def plot_cilia_per_cell():
+ counts_left = []
+ counts_right = []
+
+ table = pd.read_csv(TABLE_PATH, sep='\t')
+ cell_ids = table['cell_id']
+ cell_ids = cell_ids[cell_ids != 0]
+ cell_ids = cell_ids[~np.isnan(cell_ids)]
+ cell_ids = cell_ids.astype('uint32')
+
+ unique_cell_ids = np.unique(cell_ids)
+
+ total_count = 0
+ for cell_id in unique_cell_ids:
+ n_cilia = np.sum(cell_ids == cell_id)
+ total_count += n_cilia
+ if cell_id in right_nephr_ids:
+ counts_right.append(n_cilia)
+ elif cell_id in left_nephr_ids:
+ counts_left.append(n_cilia)
+ else:
+ print(cell_id)
+
+ counts_right.sort(reverse=True)
+ counts_left.sort(reverse=True)
+ assert len(counts_right) == len(counts_left)
+ print("Total number of cilia:", total_count)
+ print("Right counts:")
+ print(sum(counts_right))
+ print("Left counts:")
+ print(sum(counts_left))
+
+ fig, axes = plt.subplots(2)
+ x = np.arange(7)
+
+ ax = axes[0]
+ ax.set_title('Right nephridium')
+ ax.bar(x, height=counts_right)
+ ax.set_ylabel('Cilia per cell')
+
+ ax = axes[1]
+ ax.set_title('Left nephridium')
+ ax.bar(x, height=counts_left)
+ ax.set_ylabel('Cilia per cell')
+
+ plt.show()
+
+
+if __name__ == '__main__':
+ check_cell_ids()
+ plot_cilia_per_cell()
--
GitLab