orthology works. SVG tissue scoping works. SVG legend and tooltips do…

…es not work
IGS · Jan 19, 2024 · 068617a · 068617a
1 parent 6effba6
commit 068617a
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Showing 4 changed files with 333 additions and 68 deletions.
diff --git a/lib/gear/orthology.py b/lib/gear/orthology.py
@@ -155,6 +155,14 @@ def map_single_gene(gene_symbol:str, orthomap_file: Path):
     """
     # Read HDF5 file using Pandas read_hdf
     gene_symbol_dict = create_orthology_gene_symbol_dict(orthomap_file)
+
+    # Check if case-insensitive gene symbol is in dictionary
+    gene_symbol = gene_symbol.lower()
+    for key in gene_symbol_dict.keys():
+        if gene_symbol == key.lower():
+            gene_symbol = key
+            break
+
     # NOTE: Not all genes can be mapped. Unmappable genes do not change in the original dataframe.
     return gene_symbol_dict.get(gene_symbol, None)
 
@@ -172,5 +180,12 @@ def map_multiple_genes(gene_symbols:list, orthomap_file: Path):
     # Read HDF5 file using Pandas read_hdf
     gene_symbol_dict = create_orthology_gene_symbol_dict(orthomap_file)
 
+    # Check if case-insensitive gene symbols are in dictionary
+    gene_symbols = [gene_symbol.lower() for gene_symbol in gene_symbols]
+    for key in gene_symbol_dict.keys():
+        if key.lower() in gene_symbols:
+            gene_symbols[gene_symbols.index(key.lower())] = key
+
+
     # NOTE: Not all genes can be mapped. Unmappable genes do not change in the original dataframe.
     return { gene_symbol: gene_symbol_dict[gene_symbol] for gene_symbol in gene_symbols if gene_symbol in gene_symbol_dict}
diff --git a/www/expression.html b/www/expression.html
@@ -185,10 +185,10 @@ <h4>miRNA tree</h4>
                   <div id="result-panel-options">
                     <span class="option-label pr-1">Scoring method: </span>
                     <div class="control select is-small">
-                      <select>
-                        <option>Gene scope</option>
-                        <option>Tissue scope</option>
-                        <option>Sample scope</option>
+                      <select id="svg-scoring-method">
+                        <option value="gene" selected>Gene scope</option>
+                        <option value="tissue">Tissue scope</option>
+                        <option value="dataset">Sample scope</option>
                       </select>
                     </div>
                   </div>