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statgen / fivex

Interactive eQTL visualizations
MIT License
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Use genelocator to show nearest genes to the page's variant #20

Closed pjvandehaar closed 4 years ago

pjvandehaar commented 5 years ago

Ticket: #18

abought commented 5 years ago

Interesting! I'd be very interested in using GeneLocator in lz-hosted as well. Would you mind if I sent a pull request to that repo with some suggested edits (likely tomorrowish)? Mostly cleanup + additional unit tests.

That would help us standardize how the library is called before it starts to be used in multiple places.

abought commented 5 years ago

I've sent a pull request for the gene locator changes, here: https://github.com/pjvandehaar/genelocator/pull/1/

Once we sort out the disposition of that PR, we can update this one as needed and merge too.

pjvandehaar commented 5 years ago

To see behavior with multiple overlapping genes, try http://0.0.0.0:5000/variant/19_49928702/ . For the busiest location in the genome, try http://0.0.0.0:5000/variant/5_141489121/ .

abought commented 5 years ago

This seems useful. From a styling standpoint, could we do something to collapse/relocate the list of overlapping genes? A long list forces the main page content down almost off the first screen:

Screen Shot 2019-11-06 at 5 24 01 PM

pjvandehaar commented 5 years ago
image
abought commented 5 years ago

Overall this is a style improvement; thanks!

Below is a suggested patch that does 3 things. I'm not sure about the resulting display, so thought I'd run it by you before merging. (I simplified the code, now we can add pizzazz)

  1. Uses the same representation of gene info for all 3 scenarios (the current branch has 3 logic branches: two of them show the same info in a different order, which isn't super fun to maintain)
  2. Add "missing data" safeguards to the view function, so it doesn't crash if a gene lookup fails
  3. Move some calculation logic from jinja to python: in general, it's easier to read templates if they focus on presentation and don't contain much logic

I also autoformatted the HTML a bit (which explains the "whitespace changed" lines in the diff).

Screen Shot 2019-11-07 at 12 14 01 PM

diff --git a/pheget/templates/phewas.html b/pheget/templates/phewas.html
index dee0d23..acf9c9c 100644
--- a/pheget/templates/phewas.html
+++ b/pheget/templates/phewas.html
@@ -16,6 +16,10 @@
   .padtop {
     padding-top: 20px;
   }
+
+  .text-with-definition {
+    text-decoration: dotted underline;
+  }
 </style>

 <body>
@@ -45,25 +49,15 @@
   <h1>chr{{ chrom }}:{{ "{:,}".format(pos) }} for all tissues and genes</h1>

   <div>
-    {% if nearest_genes|length == 1 %}
-      {% with gene = nearest_genes[0] %}
-        <p>{{ "Overlapping" if gene.start <= pos <= gene.end else "Nearest" }} gene:
-          <i>{{ gene.symbol }}</i> (<i>{{ gene.ensg }}</i>)
-          chr{{ gene.chrom }}:{{ "{:,}".format(gene.start) }}-{{ "{:,}".format(gene.end) }}</p>
-      {% endwith %}
-    {% elif nearest_genes|length <= 5 %}
-      <p style="margin-bottom:0">Overlapping genes:</p>
-      <ul>
-        {% for gene in nearest_genes %}
-          <li>chr{{ gene.chrom }}:{{ "{:,}".format(gene.start) }}-{{ "{:,}".format(gene.end) }} <i>{{ gene.symbol }}</i>
-            (<i>{{ gene.ensg }}</i>)
-          </li>
-        {% endfor %}
-      </ul>
-    {% else %}
-      <p>Overlapping genes: {% for gene in nearest_genes %}<i>{{ gene.symbol }}</i>{% if not loop.last %},
-      {% endif %}{% endfor %}</p>
-    {% endif %}
+    <p>
+      {{ "Overlapping" if is_inside_gene else "Nearest" }} gene(s):
+      {% for gene in nearest_genes %}
+        <span class="text-with-definition" title="{{ gene.ensg }}">{{ gene.symbol }}</span>
+        {%- if not loop.last -%},{% endif %}
+      {% else %}
+        (no genes found)
+      {% endfor %}
+    </p>
   </div>

   <div class="btn-group btn-group-toggle" data-toggle="buttons">
diff --git a/pheget/views/variant.py b/pheget/views/variant.py
index 1cff2e9..be2a1e5 100644
--- a/pheget/views/variant.py
+++ b/pheget/views/variant.py
@@ -3,6 +3,7 @@ Variant View Page.
 """

 from flask import render_template
+from genelocator import exception as gene_exc
 from genelocator import get_genelocator

 import pheget
@@ -16,5 +17,16 @@ def variant_view(chrom_pos):
     # TODO: Allow query params to be passed from the base page to the api endpoint, so user can direct link to a
     #   custom view
     chrom, pos = parse_position(chrom_pos)
-    nearest_genes = gl.at(chrom, pos)
-    return render_template('phewas.html', chrom=chrom, pos=pos, nearest_genes=nearest_genes)
+
+    try:
+        nearest_genes = gl.at(chrom, pos)
+    except (gene_exc.NoResultsFoundException, gene_exc.BadCoordinateException):
+        nearest_genes = []
+
+    # Are the "nearest genes" nearby, or is the variant actually inside the gene?
+    # These rules are based on the defined behavior of the genes locator
+    is_inside_gene = (len(nearest_genes) > 1 or
+                      (len(nearest_genes) == 1 and nearest_genes[0]['start'] <= pos <= nearest_genes[0]['end']))
+
+    return render_template('phewas.html',
+                           chrom=chrom, pos=pos, nearest_genes=nearest_genes, is_inside_gene=is_inside_gene)
pjvandehaar commented 5 years ago

That change looks great. Feel free to push it to this branch. I had never cared about codestyle enough to use {%- but I'm glad that we now have a use.

abought commented 4 years ago

That change looks great. Feel free to push it to this branch. I had never cared about codestyle enough to use {%- but I'm glad that we now have a use.

Rather than purely stylistic, it's actually a whitespace control feature: it allows me to display gene, gene2 instead of gene , gene2. Not well known but pretty handy.

abought commented 4 years ago

Merging our combined changes. Thanks again!