diff options
| -rw-r--r-- | wqflask/wqflask/marker_regression/display_mapping_results.py | 26 | ||||
| -rw-r--r-- | wqflask/wqflask/marker_regression/run_mapping.py | 7 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/mapping_results.html | 47 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/search_result_page.html | 4 | ||||
| -rw-r--r-- | wqflask/wqflask/views.py | 2 |
5 files changed, 74 insertions, 12 deletions
diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py index 3f6de2b2..08c2d750 100644 --- a/wqflask/wqflask/marker_regression/display_mapping_results.py +++ b/wqflask/wqflask/marker_regression/display_mapping_results.py @@ -74,6 +74,14 @@ DARKVIOLET = ImageColor.getrgb("darkviolet") MEDIUMPURPLE = ImageColor.getrgb("mediumpurple") # ---- END: Define common colours ---- # +# ZS: List of distinct colors for manhattan plot if user selects "varied" +COLOR_CODES = ["#FF0000", "#00FF00", "#0000FF", "#FFFF00", "#FF00FF", "#00FFFF", + "#000000", "#800000", "#008000", "#000080", "#808000", "#800080", + "#008080", "#808080", "#C00000", "#00C000", "#0000C0", "#C0C000", + "#C000C0", "#00C0C0", "#C0C0C0", "#400000", "#004000", "#000040"] + +DISTINCT_COLOR_LIST = [ImageColor.getrgb(color) for color in COLOR_CODES] + # ---- FONT FILES ---- # VERDANA_FILE = "./wqflask/static/fonts/verdana.ttf" VERDANA_BOLD_FILE = "./wqflask/static/fonts/verdanab.ttf" @@ -293,6 +301,12 @@ class DisplayMappingResults(object): self.plotScale = "physic" self.manhattan_plot = start_vars['manhattan_plot'] + if self.manhattan_plot: + self.color_scheme = "alternating" + if 'color_scheme' in start_vars: + self.color_scheme = start_vars['color_scheme'] + if self.color_scheme == "single": + self.manhattan_single_color = ImageColor.getrgb("#" + start_vars['manhattan_single_color']) if 'permCheck' in list(start_vars.keys()): self.permChecked = start_vars['permCheck'] @@ -2424,10 +2438,16 @@ class DisplayMappingResults(object): Yc = yZero - qtlresult['lod_score']*LRSHeightThresh/LRS_LOD_Max if self.manhattan_plot == True: - if self.selectedChr == -1 and (previous_chr_as_int % 2 == 1): - point_color = RED + if self.color_scheme == "single": + point_color = self.manhattan_single_color + elif self.color_scheme == "varied": + point_color = DISTINCT_COLOR_LIST[previous_chr_as_int] else: - point_color = BLUE + if self.selectedChr == -1 and (previous_chr_as_int % 2 == 1): + point_color = RED + else: + point_color = BLUE + im_drawer.text( text="5", xy=( diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py index 31d6a67c..c474e0e0 100644 --- a/wqflask/wqflask/marker_regression/run_mapping.py +++ b/wqflask/wqflask/marker_regression/run_mapping.py @@ -138,7 +138,12 @@ class RunMapping(object): mapping_results_filename = self.dataset.group.name + "_" + ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6)) self.mapping_results_path = "{}{}.csv".format(webqtlConfig.GENERATED_IMAGE_DIR, mapping_results_filename) - if start_vars['manhattan_plot'] == "true": + if start_vars['manhattan_plot']: + self.color_scheme = "alternating" + if "color_scheme" in start_vars: + self.color_scheme = start_vars['color_scheme'] + if self.color_scheme == "single": + self.manhattan_single_color = start_vars['manhattan_single_color'] self.manhattan_plot = True else: self.manhattan_plot = False diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html index 28d93542..9542c29d 100644 --- a/wqflask/wqflask/templates/mapping_results.html +++ b/wqflask/wqflask/templates/mapping_results.html @@ -40,6 +40,9 @@ <input type="hidden" name="use_loco" value="{{ use_loco }}"> <input type="hidden" name="selected_chr" value="{{ selectedChr }}"> <input type="hidden" name="manhattan_plot" value="{{ manhattan_plot }}"> + {% if manhattan_plot == True %} + <input type="hidden" name="color_scheme" value="alternating"> + {% endif %} <input type="hidden" name="num_perm" value="{{ nperm }}"> <input type="hidden" name="perm_info" value=""> <input type="hidden" name="perm_strata" value="{{ perm_strata }}"> @@ -55,7 +58,7 @@ <input type="hidden" name="wanted_inputs" value=""> <input type="hidden" name="form_url" value="/run_mapping"> - <div class="container"> + <div class="container" style="min-width: 1400px;"> <div class="col-xs-5"> <h2>Map Viewer: Whole Genome</h2><br> <b>Population:</b> {{ dataset.group.species|capitalize }} {{ dataset.group.name }}<br> @@ -77,7 +80,7 @@ <table> <tr> <td><b>Chr: </b></td> - <td> + <td style="padding: 5px;"> <select name="chromosomes" size="1"> {% for chr in ChrList %} <option value="{{ chr[1] }}" {% if (chr[1] + 1) == selectedChr %}selected{% endif %}>{{ chr[0] }}</option> @@ -87,7 +90,7 @@ </td> </tr> <tr> - <td><b>View: </b></td> + <td ><b>View: </b></td> <td style="padding: 5px;"> <input type="text" name="startMb" size="7" value="{% if startMb != -1 %}{{ startMb }}{% endif %}"> to <input type="text" name="endMb" size="7" value="{% if endMb != -1 %}{{ endMb }}{% endif %}"> </td> @@ -114,11 +117,31 @@ </tr> <tr> <td><b>Width: </b></td> - <td> + <td style="padding: 5px;"> <input type="text" name="graphWidth" value="{% if graphWidth is defined %}{{ graphWidth }}{% else %}1600{% endif %}" size="5"><span style="font-size: 12px;"> pixels (minimum=900)</span> </td> </tr> </table> + {% if manhattan_plot == True and selectedChr == -1 %} + <table style="margin-top: 10px;"> + <tr> + <td> + <b>Manhattan Plot Color Scheme: </b> + </td> + <td> + <select id="color_scheme"> + <option value="alternating" {% if color_scheme == "alternating" %}selected{% endif %}>Alternating</option> + <option value="varied" {% if color_scheme == "varied" %}selected{% endif %}>Varied by Chr</option> + <option value="single" {% if color_scheme == "single" %}selected{% endif %}>Single Color</option> + </select> + </td> + <td> + <input name="manhattan_single_color" type="hidden" id="point_color" value={% if manhattan_single_color %}{{ manhattan_single_color }}{% else %}"#D9D9D9"{% endif %}> + <button style="display: none; margin-left: 5px;" id="point_color_picker" class="jscolor {valueElement: 'point_color'}">Choose Color</button> + </td> + </tr> + </table> + {% endif %} </div> <div class="col-xs-4" style="padding: 0px;"> {% if (mapping_method == "reaper" or mapping_method == "rqtl_geno") and nperm > 0 %} @@ -328,6 +351,9 @@ <script type="text/javascript" src="{{ url_for('js', filename='underscore-string/underscore.string.min.js') }}"></script> <script type="text/javascript" src="{{ url_for('js', filename='d3-tip/d3-tip.js') }}"></script> <script type="text/javascript" src="/static/new/js_external/plotly-latest.min.js"></script> + {% if manhattan_plot == True and selectedChr == -1 %} + <script type="text/javascript" src="/static/new/js_external/jscolor.js"></script> + {% endif %} <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.min.js') }}"></script> <script language="javascript" type="text/javascript" src="https://cdn.datatables.net/buttons/1.0.0/js/dataTables.buttons.min.js"></script> @@ -423,7 +449,7 @@ var mapping_input_list = ['temp_uuid', 'trait_id', 'dataset', 'tool_used', 'form_url', 'method', 'transform', 'trimmed_markers', 'selected_chr', 'chromosomes', 'mapping_scale', 'score_type', 'suggestive', 'significant', 'num_perm', 'permCheck', 'perm_output', 'perm_strata', 'categorical_vars', 'num_bootstrap', 'bootCheck', 'bootstrap_results', - 'LRSCheck', 'covariates', 'maf', 'use_loco', 'manhattan_plot', 'control_marker', 'control_marker_db', 'do_control', 'genofile', + 'LRSCheck', 'covariates', 'maf', 'use_loco', 'manhattan_plot', 'color_scheme', 'manhattan_single_color', 'control_marker', 'control_marker_db', 'do_control', 'genofile', 'pair_scan', 'startMb', 'endMb', 'graphWidth', 'lrsMax', 'additiveCheck', 'showSNP', 'showGenes', 'viewLegend', 'haplotypeAnalystCheck', 'mapmethod_rqtl_geno', 'mapmodel_rqtl_geno', 'temp_trait', 'group', 'species', 'reaper_version', 'primary_samples', 'n_samples'] @@ -449,10 +475,21 @@ remap = function() { $('input[name=selected_chr]').val($('select[name=chromosomes]').val()); + $('input[name=color_scheme]').val($('select#color_scheme').val()); $('#marker_regression_form').attr('action', '/loading'); return $('#marker_regression_form').submit(); }; + {% if manhattan_plot == True and selectedChr == -1 %} + $('#color_scheme').change(function(){ + if ($(this).val() == "single"){ + $('#point_color_picker').show(); + } else { + $('#point_color_picker').hide(); + } + }); + {% endif %} + {% if mapping_method != "gemma" and mapping_method != "plink" %} $('#download_perm').click(function(){ perm_info_dict = { diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html index 8e2b06a4..9a28a78e 100644 --- a/wqflask/wqflask/templates/search_result_page.html +++ b/wqflask/wqflask/templates/search_result_page.html @@ -2,9 +2,9 @@ {% block title %}Search Results{% endblock %} {% block css %} <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" /> + <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='fontawesome/css/font-awesome.min.css') }}" /> <link rel="stylesheet" type="text/css" href="{{ url_for('js', filename='DataTablesExtensions/scroller/css/scroller.dataTables.min.css') }}"> <link rel="stylesheet" type="text/css" href="{{ url_for('js', filename='DataTablesExtensions/buttonStyles/css/buttons.dataTables.min.css') }}"> - <link rel="stylesheet" type="text/css" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.1/css/all.min.css"> <link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" /> <link rel="stylesheet" type="text/css" href="static/new/css/trait_list.css" /> {% endblock %} @@ -440,8 +440,6 @@ 'processing': 'Loading...' } } ); - - console.timeEnd("Creating table"); $('.toggle-vis').on( 'click', function (e) { e.preventDefault(); diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index bf2e9026..5f6a431d 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -718,6 +718,8 @@ def mapping_results_page(): 'maf', 'use_loco', 'manhattan_plot', + 'color_scheme', + 'manhattan_single_color', 'control_marker', 'control_marker_db', 'do_control', |