@sjcrh/proteinpaint-server 2.86.0 → 2.87.0

package/utils/gsea.py

@@ -10,7 +10,7 @@ import numpy as np
 import pandas as pd
             
 def extract_symbols(x):
-   return x['symbol'] 
+   return x['symbol']
 
 def extract_plot_data(signature, geneset, library, result, center=True):
    signature = signature.copy()
@@ -48,6 +48,7 @@ try:
             genes=json_object['genes']
             fold_change=json_object['fold_change']
             table_name=json_object['geneset_group']
+            filter_non_coding_genes=json_object['filter_non_coding_genes']
             df = {'Genes': genes, 'fold_change': fold_change}
             signature=pd.DataFrame(df)
             db=json_object['db']
@@ -59,10 +60,19 @@ try:
             
             # SQL query to select all data from the table
             query = f"select id from terms where parent_id='" + table_name  + "'"
-            
             # Execute the SQL query
             cursor.execute(query)
-            
+            if filter_non_coding_genes == True:
+                 # SQL query to code all the protein coding genes
+                 coding_genes_query = f"select * from codingGenes"
+                 genedb = json_object['genedb']
+                 gene_conn = sqlite3.connect(genedb)
+                 gene_cursor = gene_conn.cursor()
+                 gene_cursor.execute(coding_genes_query)
+                 coding_genes_list=gene_cursor.fetchall()
+                 coding_genes_list=list(map(lambda x: x[0],coding_genes_list))
+                 signature=signature[signature['Genes'].isin(coding_genes_list)]
+                 
             # Fetch all rows from the executed SQL query
             rows = cursor.fetchall()
             

package/utils/plotBrainImaging.py

@@ -1,69 +1,108 @@
 import nibabel as nib  # Library for loading data from neuroimaging file formats such as NIfTI
 import matplotlib.pyplot as plt
+import matplotlib.colors as mcolors
+import matplotlib.cm as cm
 import numpy as np
 import sys
 import io
+import json
 
 if len(sys.argv) <= 1:
-	print('python3 '+sys.argv[0]+' <path/to/template/file> <path/to/label/file> indexL indexF, indexT')
+	print('python3 '+sys.argv[0]+' <path/to/template/file> plane index filesJson.\n filesJson: dictionary containg sample files and color per category).\nplane: L (left, sagittal), F (front, coronal), T (top, axial)')
+	sys.exit(1)
+
+plane = sys.argv[2]
+if(plane != 'L' and plane != 'F' and plane != 'T'):
+	print('Invalid plane')
+	sys.exit(1)
+index = sys.argv[3]
+
+if(len(index) == 0):
+	print('Need to provide index')
 	sys.exit(1)
 
 templateFile = sys.argv[1]
-labelFile = sys.argv[2]
 
 # load data from nifti files 
 template = nib.load(templateFile).get_fdata()
-labels = nib.load(labelFile).get_fdata()
-labels = np.ma.masked_where(labels == 0, labels) # Mask labels where they are 0
-
-l = int(sys.argv[3]) if len(sys.argv) > 3 else 70
-f = int(sys.argv[4]) if len(sys.argv) > 4 else 110
-t = int(sys.argv[5]) if len(sys.argv) > 5 else 80
-
-# extract slices l (left, sagittal), f (front, coronal), t (top, axial) from the template and label data
-left_slice = template[l,:,:]
-front_slice = template[:,f,:]
-top_slice = template[:,:,t]
-
-left_label = labels[l,:,:]
-front_label = labels[:,f,:]
-top_label = labels[:,:,t]
-
-
-# adjust the orientation of the plots by flipping and rotating
-left_slice = np.rot90(left_slice)
-left_label = np.rot90(left_label)
-
-front_slice = np.flip(np.rot90(front_slice),axis=1)
-front_label = np.flip(np.rot90(front_label),axis=1)
-
-top_slice = np.flip(np.rot90(top_slice),axis=1)
-top_label = np.flip(np.rot90(top_label),axis=1)
-
-
-# create three subplots for sagittal, coronal and axial plane
-fig, ax = plt.subplots(1, 3)
-vmin = 0
-vmax = 100
-alpha = 0.5
-ax[0].imshow(left_slice, 'gray', filternorm=False, vmin=vmin, vmax=vmax)
-ax[0].imshow(left_label, 'jet', alpha=alpha, filternorm=False,vmin=0,vmax=102)
-ax[0].axis('off')
-ax[0].text(0, 0.5, 'P', fontsize=12, color='white', ha='center', va='center', transform=ax[0].transAxes)
-ax[0].text(0.5, 1, 'S', fontsize=12, color='white', ha='center', va='center', transform=ax[0].transAxes)
-
-ax[1].imshow(front_slice, 'gray', filternorm=False, vmin=vmin, vmax=vmax)
-ax[1].imshow(front_label, cmap='jet', alpha=alpha, filternorm=False,vmin=0,vmax=102)
-ax[1].axis('off')
-ax[1].text(0, 0.5, 'R', fontsize=12, color='white', ha='center', va='center', transform=ax[1].transAxes)
-ax[1].text(0.5, 1, 'S', fontsize=12, color='white', ha='center', va='center', transform=ax[1].transAxes)
-
-ax[2].imshow(top_slice, 'gray', filternorm=False, vmin=vmin, vmax=vmax)
-ax[2].imshow(top_label, cmap='jet', alpha=alpha, filternorm=False,vmin=0,vmax=102)
-ax[2].axis('off')
-ax[2].text(0, 0.5, 'R', fontsize=12, color='white', ha='center', va='center', transform=ax[2].transAxes)
-ax[2].text(0.5, 1, 'A', fontsize=12, color='white', ha='center', va='center', transform=ax[2].transAxes)
-fig.subplots_adjust(wspace=0, hspace=0)
+
+vmaxSamples = sys.argv[4]
+
+if(len(vmaxSamples) == 0):
+	print('Need to provide max samples for normalization')
+	sys.exit(1)
+vmaxSamples = int(vmaxSamples)
+
+sampleFiles = json.loads(sys.argv[5])
+
+
+index = int(index)
+#  (left, sagittal), f (front, coronal), t (top, axial) 
+if plane == 'L':
+	slice = template[index,:,:]
+	slice = np.rot90(slice)
+elif plane == 'F':
+	slice = template[:,index,:]
+	slice = np.flip(np.rot90(slice),axis=1)
+
+else:# plane == 'T'
+	slice = template[:,:,index]
+	slice = np.flip(np.rot90(slice),axis=1)
+
+fig, ax = plt.subplots(1, 1)
+ax.imshow(slice, 'gray', filternorm=False, vmin=0, vmax=100)
+
+for key, value in sampleFiles.items():
+	if(len(value["samples"]) == 0) :
+		continue
+	# Load all sample files
+	sample_data = [nib.load(file_path).get_fdata() for file_path in value["samples"]]
+
+	# Initialize the result array with zeros
+	labels = np.zeros_like(sample_data[0])
+
+	# Sum all sample data
+	for data in sample_data:
+		labels += data
+
+	labels = np.ma.masked_where(labels == 0, labels) # Mask labels where they are 0
+
+
+	index = int(index)
+	#  (left, sagittal), f (front, coronal), t (top, axial) 
+	if plane == 'L':
+		label = labels[index,:,:]
+		label = np.rot90(label)
+	elif plane == 'F':
+		label = labels[:,index,:]
+		label = np.flip(np.rot90(label),axis=1)
+	else:# plane == 'T'
+		label = labels[:,:,index]
+		label = np.flip(np.rot90(label),axis=1)
+		
+
+
+	# create three subplots for sagittal, coronal and axial plane
+	vmin = 0
+	vmax = 100
+	alpha = 0.6
+
+	color = value['color']
+	print(color)
+	cmap = mcolors.LinearSegmentedColormap.from_list('my_cmap', ['white', color])
+	ax.imshow(label, cmap, alpha=alpha, filternorm=False,vmin=0,vmax=vmaxSamples)
+	ax.axis('off')
+
+# Create the color bar
+# if showLegend == 1:
+# 	# Create a color bar without changing figure size
+# 	norm = mcolors.Normalize(vmin=0, vmax=vmaxSamples)
+# 	sm = plt.cm.ScalarMappable(cmap=cmap, norm=norm)
+
+# 	cbar = plt.colorbar(sm, ax=ax, orientation='vertical', fraction=0.01, pad=0.05, alpha=alpha)
+# 	cbar.set_label('Combined Intensity', color='white', fontsize=6, labelpad=-10)
+# 	cbar.ax.text(0.5, 1.0001, vmaxSamples, ha='center', va='bottom', transform=cbar.ax.transAxes, color='white', fontsize=6)
+# 	cbar.ax.text(0.5, -0.0001, 0, ha='center', va='top', transform=cbar.ax.transAxes, color='white', fontsize=6)
 
 # Output the image data to stdout
 buf = io.BytesIO()