From 51383c96dc275f4462716398f9ec665fbd84802a Mon Sep 17 00:00:00 2001 From: zsloan Date: Fri, 2 Mar 2018 17:59:28 +0000 Subject: Added option to display selected covariates for GEMMA mapping Changed layout/appearance of mapping options Partially fixed issue with deleting collections Changes to correlation table still in progress; having trouble getting tabulator to load JSON --- wqflask/wqflask/collect.py | 7 +- wqflask/wqflask/marker_regression/gemma_mapping.py | 4 +- .../javascript/get_covariates_from_collection.js | 5 + .../wqflask/static/new/javascript/show_trait.js | 3 +- wqflask/wqflask/templates/collections/list.html | 12 +- wqflask/wqflask/templates/correlation_page.html | 43 +++-- .../templates/show_trait_mapping_tools.html | 208 ++++++++++----------- 7 files changed, 146 insertions(+), 136 deletions(-) diff --git a/wqflask/wqflask/collect.py b/wqflask/wqflask/collect.py index 2f6c3a96..0f72b29d 100644 --- a/wqflask/wqflask/collect.py +++ b/wqflask/wqflask/collect.py @@ -349,8 +349,11 @@ def delete_collection(): db_session.delete(uc) db_session.commit() else: - collection_name = params['collection_name'] - user_manager.AnonUser().delete_collection(collection_name) + if "collection_name" in params: + collection_name = params['collection_name'] + else: + for this_collection in params['uc_id'].split(":"): + user_manager.AnonUser().delete_collection(this_collection) flash("We've deleted the collection: {}.".format(collection_name), "alert-info") diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py index 233a5c76..7563eb2c 100644 --- a/wqflask/wqflask/marker_regression/gemma_mapping.py +++ b/wqflask/wqflask/marker_regression/gemma_mapping.py @@ -235,7 +235,7 @@ def parse_loco_output(this_dataset, gwa_output_filename): else: marker['chr'] = line.split("\t")[0] marker['Mb'] = float(line.split("\t")[2]) / 1000000 - marker['p_value'] = float(line.split("\t")[10]) + marker['p_value'] = float(line.split("\t")[11]) if math.isnan(marker['p_value']) or (marker['p_value'] <= 0): marker['lod_score'] = 0 #marker['lrs_value'] = 0 @@ -245,6 +245,6 @@ def parse_loco_output(this_dataset, gwa_output_filename): marker_obs.append(marker) included_markers.append(line.split("\t")[1]) - p_values.append(float(line.split("\t")[10])) + p_values.append(float(line.split("\t")[11])) return marker_obs \ No newline at end of file diff --git a/wqflask/wqflask/static/new/javascript/get_covariates_from_collection.js b/wqflask/wqflask/static/new/javascript/get_covariates_from_collection.js index 92e2b13b..f2e694d8 100644 --- a/wqflask/wqflask/static/new/javascript/get_covariates_from_collection.js +++ b/wqflask/wqflask/static/new/javascript/get_covariates_from_collection.js @@ -24,6 +24,7 @@ collection_click = function() { submit_click = function() { var covariates_string = ""; + var covariates_display_string = ""; $('#collections_holder').find('input[type=checkbox]:checked').each(function() { var this_dataset, this_trait; this_trait = $(this).parents('tr').find('.trait').text(); @@ -31,12 +32,15 @@ submit_click = function() { this_dataset = $(this).parents('tr').find('.dataset').text(); console.log("this_dataset is:", this_dataset); covariates_string += this_trait + ":" + this_dataset + "," + covariates_display_string += this_trait + "\n" }); // Trim the last comma covariates_string = covariates_string.substring(0, covariates_string.length - 1) + //covariates_display_string = covariates_display_string.substring(0, covariates_display_string.length - 2) console.log("COVARIATES:", covariates_string) $("input[name=covariates]").val(covariates_string) + $(".selected_covariates").val(covariates_display_string) return $.colorbox.close(); }; @@ -46,6 +50,7 @@ trait_click = function() { trait = $(this).parent().find('.trait').text(); dataset = $(this).parent().find('.dataset').text(); $("input[name=covariates]").val(trait + ":" + dataset) + $(".selected_covariates").text(trait) return $.colorbox.close(); }; diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js index 099d8010..df10c060 100644 --- a/wqflask/wqflask/static/new/javascript/show_trait.js +++ b/wqflask/wqflask/static/new/javascript/show_trait.js @@ -88,7 +88,8 @@ }; })(this)); $("#remove_covariates").click(function () { - $("input[name=covariates]").val("") + $("input[name=covariates]").val("") + $(".selected_covariates").val("") }); d3.select("#clear_compare_trait").on("click", (function(_this) { return function() { diff --git a/wqflask/wqflask/templates/collections/list.html b/wqflask/wqflask/templates/collections/list.html index ad72052e..e7f3229b 100644 --- a/wqflask/wqflask/templates/collections/list.html +++ b/wqflask/wqflask/templates/collections/list.html @@ -26,13 +26,13 @@ {% endif %}
-
- -
+
+ +
- +

@@ -51,7 +51,11 @@ {% for uc in collections %} + {% if g.user_session.user_ob %} + {% else %} + + {% endif %} {{ loop.index }} {% if g.user_session.user_ob %} {{ uc.name }} diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html index 1254ea6a..0d305559 100644 --- a/wqflask/wqflask/templates/correlation_page.html +++ b/wqflask/wqflask/templates/correlation_page.html @@ -275,29 +275,32 @@ {% if target_dataset.type == "ProbeSet" %} - var json_array = new Array(); + var json_array = []; for (i=0; i < table_json.length; i++){ - json_array.push({ - checkbox: table_json[i]["checkbox"], - index: table_json[i]["index"], - trait_id: table_json[i]["trait_id"], - symbol: table_json[i]["symbol"], - description: table_json[i]["description"], - location: table_json[i]["location"], - mean: table_json[i]["mean"], - lrs_score: table_json[i]["lrs_score"], - lrs_location: table_json[i]["lrs_location"], - additive: table_json[i]["additive"], - sample_r: table_json[i]["sample_r"], - num_overlap: table_json[i]["num_overlap"], - sample_p: table_json[i]["sample_p"], - lit_corr: table_json[i]["lit_corr"], - tissue_corr: table_json[i]["tissue_corr"] - }); - console.log("JSON_DATA:", json_array); + this_array = json_array + + var row_dict = {}; + row_dict.checkbox = table_json[i]["checkbox"] + row_dict.index = table_json[i]["index"] + row_dict.trait_id = table_json[i]["trait_id"] + row_dict.symbol = table_json[i]["symbol"] + row_dict.description = table_json[i]["description"] + row_dict.location = table_json[i]["location"] + row_dict.mean = table_json[i]["mean"] + row_dict.lrs_score = table_json[i]["lrs_score"] + row_dict.lrs_location = table_json[i]["lrs_location"] + row_dict.additive = table_json[i]["additive"] + row_dict.sample_r = table_json[i]["sample_r"] + row_dict.num_overlap = table_json[i]["num_overlap"] + row_dict.sample_p = table_json[i]["sample_p"] + row_dict.lit_corr = table_json[i]["lit_corr"] + row_dict.tissue_corr = table_json[i]["tissue_corr"] + this_array.push(row_dict); + json_array.concat(this_array); + //console.log("JSON_ARRAY:", json_array); } - //console.log("JSON_DATA:", json_array) + console.log("JSON_DATA:", json_array) $("#trait_table").tabulator({ data: json_array, diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html index dcec2b9e..ab2e2aae 100644 --- a/wqflask/wqflask/templates/show_trait_mapping_tools.html +++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html @@ -1,6 +1,6 @@
{% if (use_pylmm_rqtl and dataset.group.species != "human") or use_plink_gemma %} -
+
    @@ -38,11 +38,11 @@ {# if use_pylmm_rqtl and not use_plink_gemma and dataset.group.species != "human" #} {% if dataset.group.mapping_id == "1" %}
    -
    +
    {% if genofiles and genofiles|length>0 %}
    - -
    + +
    - -
    + +
    +
    - - + +
    + + {% endif %} +
    +
    +
    + +
    + +
    - +
    {% if genofiles and genofiles|length>0 %}
    - -
    + +
    - -
    + +
    - -
    + +
    {% if dataset.type == 'ProbeSet' and this_trait.locus_chr != "" %} {% else %} @@ -162,8 +184,8 @@
    - -
    + +
    -
    -
    - +
    + +
    +
    @@ -189,8 +212,8 @@
    {% if genofiles and genofiles|length>0 %}
    - -
    + +
    + +
    +
    -
    - -
    + +
    {% if dataset.type == 'ProbeSet' and this_trait.locus_chr != "" %} {% else %} @@ -228,8 +248,8 @@
    - -
    + +
    - -
    + +
    -
    -
    - +
    + +
    +
    @@ -295,8 +316,8 @@
    {% if genofiles and genofiles|length>0 %}
    - -
    + +
    {% for item in genofiles %} @@ -365,29 +354,34 @@
    {% endif %}
    - -
    + +
    -
    - -
    - - + +
    + {% if g.user_session.user_ob and (g.user_session.user_ob.display_num_collections() == "") %} + No collections available. Please add traits to a collection to use them as covariates. + {% elif g.cookie_session.display_num_collections() == "" %} + No collections available. Please add traits to a collection to use them as covariates. + {% else %} +
    + + +
    + + {% endif %} +
    -
    - -
    -
    +
    + +
    +
    @@ -416,7 +410,7 @@
    -
    +
    {% if dataset.group.mapping_id == "1" %}
    Interval Mapping
    -- cgit v1.2.3