Merge pull request #72 from Eeeeelias/master

Improve output visualisations

container/domain/Process/nease_output.py

@@ -251,25 +251,53 @@ def visualise_path(events, pathway, k):
 
 
 def create_plot(terms, pvalues, cut_off, filename):
-    # plt.style.use('ggplot')
-    plt.barh(terms[::-1], pvalues[::-1])
-    plt.axvline(x=cut_off, color='r', linestyle='--')
-    plt.xlabel('-log10(adjusted p-value)')
-    plt.ylabel('Terms')
-    # explain the red line in the legend
-    plt.legend(['Cut-off', 'Adjusted p-value'])
+    # add line break to terms that are longer than 50 characters
+    terms = cut_long_terms(terms)
 
+    colors = ['#344552', '#355871', '#366B91', '#377DB0', '#448FC5', '#5E9FCD', '#78B0D5', '#92C0DD']
+    plt.figure(figsize=(12, 5))
+    plt.grid(color='#D2D2D2', linestyle='-', zorder=0)
+
+    plt.barh(terms[::-1], pvalues[::-1], color=colors[::-1], zorder=3)
+    plt.axvline(x=cut_off, color='red', linestyle='--', linewidth=1.5, zorder=5)
+    plt.ylabel("Terms", fontsize=12)
+    plt.xlabel("-log10(adjusted p-value)", fontsize=12)
+
+    plt.legend(['Cut-off', 'Adjusted p-value'], fontsize=10, frameon=True)
+
+    # Edit the spines for a cleaner look
     ax = plt.gca()
+    ax.tick_params(bottom=False)
+    ax.tick_params(left=False)
+    ax.spines[['left', 'bottom']].set_color('#D2D2D2')
+    ax.spines[['left', 'bottom']].set_linewidth(2)
     ax.spines['top'].set_visible(False)
     ax.spines['right'].set_visible(False)
 
+    plt.tight_layout()
+
     plt.savefig(f"{filename}_thumb.jpg", bbox_inches='tight')
     plt.savefig(f"{filename}.jpg", bbox_inches='tight', dpi=1200)
     # flush the plot
     plt.clf()
     plt.close()
 
 
+def cut_long_terms(terms):
+    cut_terms = []
+    for term in terms:
+        if len(term) > 50:
+            # find the first space after the 50th character
+            space_index = term.find(' ', 50)
+            if space_index == -1:
+                cut_terms.append(term)
+            else:
+                cut_terms.append(term[:space_index] + '\n' + term[space_index + 1:])
+        else:
+            cut_terms.append(term)
+    return cut_terms
+
+
 def change_save_timing(run_id, days):
     mapping = NeaseSaveLocationMapping.objects.get(run_id=run_id)
     current_days_folder = mapping.get_number_of_saved_for_days()

container/domain/nease/functions.py

@@ -522,27 +522,36 @@ def stats_domains(affecting_percentage,
     # pie chart parameters
     ratios_pie = [affecting_percentage, 1 - affecting_percentage]
     labels_pie = ['Affecting protein features', 'Not affecting any feature']
-    pie_colors = ['#1f78b4', '#fe7f0e']
+    pie_colors = ['#377DB0', '#E68A00']
+
     ax1.set_facecolor('white')
     ax1.pie(ratios_pie, labels=labels_pie, autopct='%1.1f%%', startangle=0, wedgeprops={'edgecolor': 'white'},
-            colors=pie_colors)
-    ax1.set_title("Genes with AS affecting protein features")
+            colors=pie_colors, textprops={'fontsize': 12, 'color': 'black'})  # Set font size and color for percentages
+    ax1.set_title("Genes with AS affecting protein features", fontsize=14)
 
     ratios_bar = [round(elm_number / number_of_features, 2) * 100, round(pdb_number / number_of_features, 2) * 100,
               round(domain_number / number_of_features, 2) * 100]
 
     labels_bar = ['Linear motifs', 'Residues', 'Domains']
 
-    colors = ['#2ba8fc', '#2284c6', '#15547e']
+    colors = ['#344552', '#377DB0', '#92C0DD'][::-1]
 
     ax2.set_facecolor('white')
     ax2.barh(labels_bar, ratios_bar, color=colors)
     ax2.set_xlim(0, 100)
-    ax2.set_title('Affected features')
+    ax2.set_title('Affected features', fontsize=14)
+
+    # Remove unnecessary spines and ticks, while keeping the clean look
+    ax2.tick_params(bottom=False)
+    ax2.tick_params(left=False)
+    ax2.spines[['left', 'bottom']].set_color('#D2D2D2')
+    ax2.spines[['left', 'bottom']].set_linewidth(2)
+    ax2.spines['right'].set_visible(False)
+    ax2.spines['bottom'].set_visible(False)
+    ax2.spines['top'].set_visible(False)
     ax2.grid(False)
     ax2.yaxis.set_ticks_position('none')
-    ax2.spines[['right', 'top']].set_visible(False)
-    ax2.spines[['left', 'bottom']].set_visible(True)
+    ax2.xaxis.set_visible(False)
 
     for i, v in enumerate(ratios_bar):
         ax2.text(v + 1, i, f"{v:.1f}%", va='center', color='black', fontweight='bold')