From 3379fd0f0f829643651b89315e1a2e98cecf1652 Mon Sep 17 00:00:00 2001 From: zsloan Date: Mon, 12 Nov 2018 22:17:32 +0000 Subject: Added change to remove qtlreaper use from correlation and prevent the inconsistent error Added change to change maf depending upon number of sample values Committing in-process changes to how sample table is built on trait page (to make it look better and more compact) : --- wqflask/wqflask/correlation/show_corr_results.py | 2 +- wqflask/wqflask/show_trait/show_trait.py | 26 +++++++++++++++------- wqflask/wqflask/static/new/css/show_trait.css | 17 ++++++++++++++ wqflask/wqflask/templates/show_trait.html | 4 ++-- .../wqflask/templates/show_trait_edit_data.html | 8 +++---- .../templates/show_trait_mapping_tools.html | 2 +- 6 files changed, 43 insertions(+), 16 deletions(-) diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py index 9f3f7982..0b2875cc 100644 --- a/wqflask/wqflask/correlation/show_corr_results.py +++ b/wqflask/wqflask/correlation/show_corr_results.py @@ -99,7 +99,7 @@ class CorrelationResults(object): else: helper_functions.get_species_dataset_trait(self, start_vars) - self.dataset.group.read_genotype_file() + #self.dataset.group.read_genotype_file() corr_samples_group = start_vars['corr_samples_group'] diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py index f75302f6..34447853 100644 --- a/wqflask/wqflask/show_trait/show_trait.py +++ b/wqflask/wqflask/show_trait/show_trait.py @@ -188,13 +188,23 @@ class ShowTrait(object): self.stats_table_width, self.trait_table_width = get_table_widths(self.sample_groups, self.has_num_cases) - #ZS: Needed to know whether to display bar chart + #ZS: Needed to know whether to display bar chart + get max sample name length in order to set table column width self.num_values = 0 + max_samplename_width = 1 for group in self.sample_groups: for sample in group.sample_list: + if len(sample.name) > max_samplename_width: + max_samplename_width = len(sample.name) if sample.display_value != "x": self.num_values += 1 + sample_column_width = max_samplename_width * 8 + + if self.num_values >= 500: + self.maf = 0.01 + else: + self.maf = 0.05 + trait_symbol = None if not self.temp_trait: if self.this_trait.symbol: @@ -208,6 +218,7 @@ class ShowTrait(object): sample_lists = sample_lists, attribute_names = self.sample_groups[0].attributes, num_values = self.num_values, + sample_column_width = sample_column_width, temp_uuid = self.temp_uuid) self.js_data = js_data @@ -368,15 +379,14 @@ def get_table_widths(sample_groups, has_num_cases=False): if len(sample_groups) > 1: stats_table_width = 450 - trait_table_width = 25 + trait_table_width = 380 if sample_groups[0].se_exists(): - trait_table_width += 15 + trait_table_width += 70 if has_num_cases: - trait_table_width += 5 - if (trait_table_width + len(sample_groups[0].attributes)*10) > 100: - trait_table_width = 100 - else: - trait_table_width += len(sample_groups[0].attributes)*10 + trait_table_width += 30 + trait_table_width += len(sample_groups[0].attributes)*40 + + trait_table_width = str(trait_table_width) + "px" return stats_table_width, trait_table_width diff --git a/wqflask/wqflask/static/new/css/show_trait.css b/wqflask/wqflask/static/new/css/show_trait.css index 135a7643..69c4418a 100644 --- a/wqflask/wqflask/static/new/css/show_trait.css +++ b/wqflask/wqflask/static/new/css/show_trait.css @@ -12,4 +12,21 @@ div.sample_group { .js-plotly-plot .plotly .modebar { left: 100px; +} + +table.dataTable thead th{ + border-right: 1px solid white; + color: white; + background-color: #369; +} + +table.dataTable thead .sorting_asc { + background-image: url("../packages/DataTables/images/sort_asc_disabled.png"); +} +table.dataTable thead .sorting_desc { + background-image: url("../packages/DataTables/images/sort_desc_disabled.png"); +} + +table.dataTable tbody td { + padding: 3px 20px 1px 10px; } \ No newline at end of file diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html index ef05e321..8726226c 100644 --- a/wqflask/wqflask/templates/show_trait.html +++ b/wqflask/wqflask/templates/show_trait.html @@ -1,7 +1,6 @@ {% extends "base.html" %} {% block title %}Trait Data and Analysis{% endblock %} {% block css %} - @@ -12,6 +11,7 @@ + {% endblock %} {% block content %} @@ -192,7 +192,7 @@ "columns": [ { "bSortable": false }, { "type": "natural" }, - { "type": "natural", "width": "25%" }, + { "type": "natural", "width": js_data.sample_column_width}, { "type": "cust-txt" }, { "bSortable": false }, { "type": "cust-txt" }{% if has_num_cases %}, diff --git a/wqflask/wqflask/templates/show_trait_edit_data.html b/wqflask/wqflask/templates/show_trait_edit_data.html index bd40946d..7ac4b2c0 100644 --- a/wqflask/wqflask/templates/show_trait_edit_data.html +++ b/wqflask/wqflask/templates/show_trait_edit_data.html @@ -86,11 +86,11 @@ {% for sample_type in sample_groups %} {% set outer_loop = loop %} -
+

{{ sample_type.header }}

- +
@@ -98,7 +98,7 @@ {% if sample_type.se_exists() %} - + {% endif %} {% if has_num_cases %} @@ -134,7 +134,7 @@ {% if sample_type.se_exists() %} - diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html index 72b3b00b..8e003897 100644 --- a/wqflask/wqflask/templates/show_trait_mapping_tools.html +++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html @@ -54,7 +54,7 @@
- +
-- cgit v1.2.3
Sample Value   SE + ±