support volcano labeling in get_volcano & improve plot_glycans_excel …

…resolution

build/lib/glycowork/motif/analysis.py

@@ -681,7 +681,8 @@ def get_ma(df_res, log2fc_thresh = 1, sig_thresh = 0.05, filepath = ''):
 
 
 def get_volcano(df_res, y_thresh = 0.05, x_thresh = 1.0,
-                 label_changed = True, x_metric = 'Log2FC', filepath = ''):
+                label_changed = True, x_metric = 'Log2FC', annotate_volcano = False,
+                filepath = ''):
   """Plots glycan differential expression results in a volcano plot\n
   | Arguments:
   | :-
@@ -690,6 +691,7 @@ def get_volcano(df_res, y_thresh = 0.05, x_thresh = 1.0,
   | x_thresh (float): absolute x metric threshold for labeling datapoints; default:1.0
   | label_changed (bool): if True, add text labels to significantly up- and downregulated datapoints; default:True
   | x_metric (string): x-axis metric; default:'Log2FC'; options are 'Log2FC', 'Effect size'
+  | annotate_volcano (bool): whether to annotate the dots in the plot with SNFG images; default: False
   | filepath (string): absolute path including full filename allows for saving the plot\n
   | Returns:
   | :-
@@ -716,6 +718,10 @@ def get_volcano(df_res, y_thresh = 0.05, x_thresh = 1.0,
   if filepath:
       plt.savefig(filepath, format = filepath.split('.')[-1], dpi = 300,
                   bbox_inches = 'tight')
+      if annotate_volcano:
+          from glycowork.motif.draw import annotate_figure
+          annotate_figure(filepath, filepath = filepath.split('.')[0]+'.pdf', scale_by_DE_res = df_res,
+                          y_thresh = y_thresh, x_thresh = x_thresh, x_metric = x_metric)
   plt.show()
 
 

build/lib/glycowork/motif/draw.py

@@ -2291,12 +2291,12 @@ def plot_glycans_excel(df, folder_filepath, glycan_col_num = 0,
       # Generate glycan image using GlycoDraw
       svg_data = GlycoDraw(glycan_structure, compact = compact).as_svg()
       # Convert SVG data to image
-      png_data = svg2png(bytestring = svg_data)
+      png_data = svg2png(bytestring = svg_data, output_width = 3000, output_height = 3000)
       img_stream = BytesIO(png_data)
       img = Image.open(img_stream)
       # Set the size of the image
       img_width, img_height = img.size
-      img = img.resize((int(img_width * scaling_factor), int(img_height * scaling_factor)), Image.LANCZOS)  
+      img = img.resize((int(img_width * scaling_factor / 5), int(img_height * scaling_factor / 5)), Image.LANCZOS)
       # Save the image to a BytesIO object
       img_stream = BytesIO()
       img.save(img_stream, format = 'PNG')

glycowork/motif/analysis.py

@@ -681,7 +681,8 @@ def get_ma(df_res, log2fc_thresh = 1, sig_thresh = 0.05, filepath = ''):
 
 
 def get_volcano(df_res, y_thresh = 0.05, x_thresh = 1.0,
-                 label_changed = True, x_metric = 'Log2FC', filepath = ''):
+                label_changed = True, x_metric = 'Log2FC', annotate_volcano = False,
+                filepath = ''):
   """Plots glycan differential expression results in a volcano plot\n
   | Arguments:
   | :-
@@ -690,6 +691,7 @@ def get_volcano(df_res, y_thresh = 0.05, x_thresh = 1.0,
   | x_thresh (float): absolute x metric threshold for labeling datapoints; default:1.0
   | label_changed (bool): if True, add text labels to significantly up- and downregulated datapoints; default:True
   | x_metric (string): x-axis metric; default:'Log2FC'; options are 'Log2FC', 'Effect size'
+  | annotate_volcano (bool): whether to annotate the dots in the plot with SNFG images; default: False
   | filepath (string): absolute path including full filename allows for saving the plot\n
   | Returns:
   | :-
@@ -716,6 +718,10 @@ def get_volcano(df_res, y_thresh = 0.05, x_thresh = 1.0,
   if filepath:
       plt.savefig(filepath, format = filepath.split('.')[-1], dpi = 300,
                   bbox_inches = 'tight')
+      if annotate_volcano:
+          from glycowork.motif.draw import annotate_figure
+          annotate_figure(filepath, filepath = filepath.split('.')[0]+'.pdf', scale_by_DE_res = df_res,
+                          y_thresh = y_thresh, x_thresh = x_thresh, x_metric = x_metric)
   plt.show()
 
 

glycowork/motif/draw.py

@@ -2291,12 +2291,12 @@ def plot_glycans_excel(df, folder_filepath, glycan_col_num = 0,
       # Generate glycan image using GlycoDraw
       svg_data = GlycoDraw(glycan_structure, compact = compact).as_svg()
       # Convert SVG data to image
-      png_data = svg2png(bytestring = svg_data)
+      png_data = svg2png(bytestring = svg_data, output_width = 3000, output_height = 3000)
       img_stream = BytesIO(png_data)
       img = Image.open(img_stream)
       # Set the size of the image
       img_width, img_height = img.size
-      img = img.resize((int(img_width * scaling_factor), int(img_height * scaling_factor)), Image.LANCZOS)  
+      img = img.resize((int(img_width * scaling_factor / 5), int(img_height * scaling_factor / 5)), Image.LANCZOS)
       # Save the image to a BytesIO object
       img_stream = BytesIO()
       img.save(img_stream, format = 'PNG')