diff --git a/external-plotting-tools.ipynb b/external-plotting-tools.ipynb new file mode 100644 index 0000000..cf968f0 --- /dev/null +++ b/external-plotting-tools.ipynb @@ -0,0 +1,2017 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Using external plotting tools with `scanpy`" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "This notebook contains some demonstrations of using external plotting tools for looking at quality control metrics and differential expression results. I'll be demonstrating some plots I find useful from [`seaborn`](https://seaborn.pydata.org) and [`hvplot`](https://hvplot.pyviz.org). As an example, we'll be looking at some PBMCs from 10x genomics." + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Setup" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "To get setup let's import our dependencies, grab the data, and create our `AnnData` object:" + ] + }, + { + "cell_type": "code", + "execution_count": 1, + "metadata": {}, + "outputs": [ + { + "data": { + "application/javascript": [ + "\n", + "(function(root) {\n", + " function now() {\n", + " return new Date();\n", + " }\n", + "\n", + " var force = true;\n", + "\n", + " if (typeof (root._bokeh_onload_callbacks) === \"undefined\" || force === true) {\n", + " root._bokeh_onload_callbacks = [];\n", + " root._bokeh_is_loading = undefined;\n", + " }\n", + "\n", + " var JS_MIME_TYPE = 'application/javascript';\n", + " var HTML_MIME_TYPE = 'text/html';\n", + " var EXEC_MIME_TYPE = 'application/vnd.bokehjs_exec.v0+json';\n", + " var CLASS_NAME = 'output_bokeh rendered_html';\n", + "\n", + " /**\n", + " * Render data to the DOM node\n", + " */\n", + " function render(props, node) {\n", + " var script = document.createElement(\"script\");\n", + " node.appendChild(script);\n", + " }\n", + "\n", + " /**\n", + " * Handle when an output is cleared or removed\n", + " */\n", + " function handleClearOutput(event, handle) {\n", + " var cell = handle.cell;\n", + "\n", + " var id = cell.output_area._bokeh_element_id;\n", + " var server_id = cell.output_area._bokeh_server_id;\n", + " // Clean up Bokeh references\n", + " if (id != null && id in Bokeh.index) {\n", + " Bokeh.index[id].model.document.clear();\n", + " delete Bokeh.index[id];\n", + " }\n", + "\n", + " if (server_id !== undefined) {\n", + " // Clean up Bokeh references\n", + " var cmd = \"from bokeh.io.state import curstate; print(curstate().uuid_to_server['\" + server_id + \"'].get_sessions()[0].document.roots[0]._id)\";\n", + " cell.notebook.kernel.execute(cmd, {\n", + " iopub: {\n", + " output: function(msg) {\n", + " var id = msg.content.text.trim();\n", + " if (id in Bokeh.index) {\n", + " Bokeh.index[id].model.document.clear();\n", + " delete Bokeh.index[id];\n", + " }\n", + " }\n", + " }\n", + " });\n", + " // Destroy server and session\n", + " var cmd = \"import bokeh.io.notebook as ion; ion.destroy_server('\" + server_id + \"')\";\n", + " cell.notebook.kernel.execute(cmd);\n", + " }\n", + " }\n", + "\n", + " /**\n", + " * Handle when a new output is added\n", + " */\n", + " function handleAddOutput(event, handle) {\n", + " var output_area = handle.output_area;\n", + " var output = handle.output;\n", + "\n", + " // limit handleAddOutput to display_data with EXEC_MIME_TYPE content only\n", + " if ((output.output_type != \"display_data\") || (!output.data.hasOwnProperty(EXEC_MIME_TYPE))) {\n", + " return\n", + " }\n", + "\n", + " var toinsert = output_area.element.find(\".\" + CLASS_NAME.split(' ')[0]);\n", + "\n", + " if (output.metadata[EXEC_MIME_TYPE][\"id\"] !== undefined) {\n", + " toinsert[toinsert.length - 1].firstChild.textContent = output.data[JS_MIME_TYPE];\n", + " // store reference to embed id on output_area\n", + " output_area._bokeh_element_id = output.metadata[EXEC_MIME_TYPE][\"id\"];\n", + " }\n", + " if (output.metadata[EXEC_MIME_TYPE][\"server_id\"] !== undefined) {\n", + " var bk_div = document.createElement(\"div\");\n", + " bk_div.innerHTML = output.data[HTML_MIME_TYPE];\n", + " var script_attrs = bk_div.children[0].attributes;\n", + " for (var i = 0; i < script_attrs.length; i++) {\n", + " toinsert[toinsert.length - 1].firstChild.setAttribute(script_attrs[i].name, script_attrs[i].value);\n", + " }\n", + " // store reference to server id on output_area\n", + " output_area._bokeh_server_id = output.metadata[EXEC_MIME_TYPE][\"server_id\"];\n", + " }\n", + " }\n", + "\n", + " function register_renderer(events, OutputArea) {\n", + "\n", + " function append_mime(data, metadata, element) {\n", + " // create a DOM node to render to\n", + " var toinsert = this.create_output_subarea(\n", + " metadata,\n", + " CLASS_NAME,\n", + " EXEC_MIME_TYPE\n", + " );\n", + " this.keyboard_manager.register_events(toinsert);\n", + " // Render to node\n", + " var props = {data: data, metadata: metadata[EXEC_MIME_TYPE]};\n", + " render(props, toinsert[toinsert.length - 1]);\n", + " element.append(toinsert);\n", + " return toinsert\n", + " }\n", + "\n", + " /* Handle when an output is cleared or removed */\n", + " events.on('clear_output.CodeCell', handleClearOutput);\n", + " events.on('delete.Cell', handleClearOutput);\n", + "\n", + " /* Handle when a new output is added */\n", + " events.on('output_added.OutputArea', handleAddOutput);\n", + "\n", + " /**\n", + " * Register the mime type and append_mime function with output_area\n", + " */\n", + " OutputArea.prototype.register_mime_type(EXEC_MIME_TYPE, append_mime, {\n", + " /* Is output safe? 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i},t.prototype.render=function(){if(this.model.visible||\"css\"!=this.model.render_mode||a.hide(this.el),this.model.visible){var t;switch(this.model.angle_units){case\"rad\":t=-this.model.angle;break;case\"deg\":t=-this.model.angle*Math.PI/180;break;default:throw new Error(\"unreachable code\")}var e=null!=this.model.panel?this.model.panel:this.plot_view.frame,i=this.plot_view.frame.xscales[this.model.x_range_name],n=this.plot_view.frame.yscales[this.model.y_range_name],r=\"data\"==this.model.x_units?i.compute(this.model.x):e.xview.compute(this.model.x),o=\"data\"==this.model.y_units?n.compute(this.model.y):e.yview.compute(this.model.y);r+=this.model.x_offset,o-=this.model.y_offset;var s=\"canvas\"==this.model.render_mode?this._canvas_text.bind(this):this._css_text.bind(this);s(this.plot_view.canvas_view.ctx,this.model.text,r,o,t)}},t}(r.TextAnnotationView);i.LabelView=s;var l=function(e){function t(t){return e.call(this,t)||this}return n.__extends(t,e),t.initClass=function(){this.prototype.type=\"Label\",this.prototype.default_view=s,this.mixins([\"text\",\"line:border_\",\"fill:background_\"]),this.define({x:[o.Number],x_units:[o.SpatialUnits,\"data\"],y:[o.Number],y_units:[o.SpatialUnits,\"data\"],text:[o.String],angle:[o.Angle,0],angle_units:[o.AngleUnits,\"rad\"],x_offset:[o.Number,0],y_offset:[o.Number,0],x_range_name:[o.String,\"default\"],y_range_name:[o.String,\"default\"]}),this.override({background_fill_color:null,border_line_color:null})},t}(r.TextAnnotation);(i.Label=l).initClass()},function(t,e,i){var n=t(391),r=t(74),o=t(200),u=t(5),s=t(15),a=function(r){function t(){return null!==r&&r.apply(this,arguments)||this}return n.__extends(t,r),t.prototype.initialize=function(t){if(r.prototype.initialize.call(this,t),this.set_data(this.model.source),\"css\"==this.model.render_mode)for(var e=0,i=this._text.length;eh(a-l)?(n=c(u(o,s),a),r=u(c(o,s),l)):(n=u(o,s),r=c(o,s)),[n,r]}throw new Error(\"user bounds '\"+e+\"' not understood\")},enumerable:!0,configurable:!0}),Object.defineProperty(t.prototype,\"rule_coords\",{get:function(){var t=this.dimension,e=(t+1)%2,i=this.ranges[0],n=this.computed_bounds,r=n[0],o=n[1],s=new Array(2),a=new Array(2),l=[s,a];return l[t][0]=Math.max(r,i.min),l[t][1]=Math.min(o,i.max),l[t][0]>l[t][1]&&(l[t][0]=l[t][1]=NaN),l[e][0]=this.loc,l[e][1]=this.loc,l},enumerable:!0,configurable:!0}),Object.defineProperty(t.prototype,\"tick_coords\",{get:function(){for(var t=this.dimension,e=(t+1)%2,i=this.ranges[0],n=this.computed_bounds,r=n[0],o=n[1],s=this.ticker.get_ticks(r,o,i,this.loc,{}),a=s.major,l=s.minor,h=[[],[]],u=[[],[]],c=[i.min,i.max],_=c[0],p=c[1],d=0;dp||(h[t].push(a[d]),h[e].push(this.loc));for(var d=0;dp||(u[t].push(l[d]),u[e].push(this.loc));return{major:h,minor:u}},enumerable:!0,configurable:!0}),Object.defineProperty(t.prototype,\"loc\",{get:function(){if(null!=this.fixed_location){if(T.isNumber(this.fixed_location))return this.fixed_location;var t=this.ranges,e=t[1];if(e instanceof a.FactorRange)return e.synthetic(this.fixed_location);throw new Error(\"unexpected\")}var i=this.ranges,n=i[1];switch(this.panel.side){case\"left\":case\"below\":return n.start;case\"right\":case\"above\":return n.end}},enumerable:!0,configurable:!0}),t}(r.GuideRenderer);(i.Axis=p).initClass()},function(t,e,i){var n=t(391),r=t(79),o=t(208),s=t(105),a=t(15),l=function(t){function e(){return null!==t&&t.apply(this,arguments)||this}return n.__extends(e,t),e.prototype._render=function(t,e,i){this._draw_group_separators(t,e,i)},e.prototype._draw_group_separators=function(t,e,i){var n,r=this.model.ranges[0],o=this.model.computed_bounds,s=o[0],a=o[1];if(r.tops&&!(r.tops.length<2)&&this.visuals.separator_line.doit){for(var l=this.model.dimension,h=(l+1)%2,u=[[],[]],c=0,_=0;_=this.scientific_limit_high||a<=this.scientific_limit_low)){n=!0;break}}var l=new Array(t.length),h=this.precision;if(null==h||f.isNumber(h))if(n)for(var u=0,c=t.length;ut.maxX&&(t.maxX=r.maxX)}for(var o=this.index.search(h.positive_y()),s=0,a=o;st.maxY&&(t.maxY=l.maxY)}return this._bounds(t)},t.prototype.get_anchor_point=function(t,e,i){var n=i[0],r=i[1];switch(t){case\"center\":return{x:this.scenterx(e,n,r),y:this.scentery(e,n,r)};default:return null}},t.prototype.sdist=function(t,e,i,n,r){var o,s;void 0===n&&(n=\"edge\"),void 0===r&&(r=!1);var a=e.length;if(\"center\"==n){var l=b.map(i,function(t){return t/2});o=new Float64Array(a);for(var h=0;h=a.length?c:a[n],l[t]=r},e=0,i=o.length;e=h.end&&(r=!0,h.end=_,(e||i)&&(h.start=_+d)),null!=p&&p<=h.start&&(r=!0,h.start=p,(e||i)&&(h.end=p-d))):(null!=_&&_>=h.start&&(r=!0,h.start=_,(e||i)&&(h.end=_+d)),null!=p&&p<=h.end&&(r=!0,h.end=p,(e||i)&&(h.start=p-d)))}}if(!(i&&r&&n))for(var f=0,v=t;fn.lod_timeout&&e.interactive_stop(n),t.request_render()},n.lod_timeout):e.interactive_stop(n)}for(var r in this.renderer_views){var o=this.renderer_views[r];if(null==this.range_update_timestamp||o instanceof T.GlyphRendererView&&o.set_data_timestamp>this.range_update_timestamp){this.update_dataranges();break}}this.model.frame.update_scales();var s=this.canvas_view.ctx,a=this.canvas.pixel_ratio;s.save(),s.scale(a,a),s.translate(.5,.5);var l=[this.frame._left.value,this.frame._top.value,this.frame._width.value,this.frame._height.value];if(this._map_hook(s,l),this._paint_empty(s,l),this.prepare_webgl(a,l),s.save(),this.visuals.outline_line.doit){this.visuals.outline_line.set_value(s);var h=l[0],u=l[1],c=l[2],_=l[3];h+c==this.canvas._width.value&&(c-=1),u+_==this.canvas._height.value&&(_-=1),s.strokeRect(h,u,c,_)}s.restore(),this._paint_levels(s,[\"image\",\"underlay\",\"glyph\"],l,!0),this.blit_webgl(a),this._paint_levels(s,[\"annotation\"],l,!0),this._paint_levels(s,[\"overlay\"],l,!1),null==this._initial_state_info.range&&this.set_initial_range(),s.restore(),this._has_finished||(this._has_finished=!0,this.notify_finished())}},t.prototype._paint_levels=function(t,e,i,n){t.save(),n&&(t.beginPath(),t.rect.apply(t,i),t.clip());for(var r={},o=0;oc&&(\"start\"==this.follow?r=n+u*c:\"end\"==this.follow&&(n=r-u*c)),[n,r]},t.prototype.update=function(t,e,i,n){if(!this.have_updated_interactively){var r=this.computed_renderers(),o=this._compute_plot_bounds(r,t);null!=n&&(o=this.adjust_bounds_for_aspect(o,n)),this._plot_bounds[i]=o;var s=this._compute_min_max(this._plot_bounds,e),a=s[0],l=s[1],h=this._compute_range(a,l),u=h[0],c=h[1];null!=this._initial_start&&(\"log\"==this.scale_hint?0this.end},enumerable:!0,configurable:!0}),t}(r.Model);(i.Range=a).initClass()},function(t,e,i){var n=t(391),r=t(183),o=t(15),s=function(e){function t(t){return e.call(this,t)||this}return n.__extends(t,e),t.initClass=function(){this.prototype.type=\"Range1d\",this.define({start:[o.Number,0],end:[o.Number,1],reset_start:[o.Number],reset_end:[o.Number]})},t.prototype._set_auto_bounds=function(){if(\"auto\"==this.bounds){var t=Math.min(this.reset_start,this.reset_end),e=Math.max(this.reset_start,this.reset_end);this.setv({bounds:[t,e]},{silent:!0})}},t.prototype.initialize=function(){e.prototype.initialize.call(this),null==this.reset_start&&(this.reset_start=this.start),null==this.reset_end&&(this.reset_end=this.end),this._set_auto_bounds()},Object.defineProperty(t.prototype,\"min\",{get:function(){return Math.min(this.start,this.end)},enumerable:!0,configurable:!0}),Object.defineProperty(t.prototype,\"max\",{get:function(){return Math.max(this.start,this.end)},enumerable:!0,configurable:!0}),t.prototype.reset=function(){this._set_auto_bounds(),this.start!=this.reset_start||this.end!=this.reset_end?this.setv({start:this.reset_start,end:this.reset_end}):this.change.emit()},t}(r.Range);(i.Range1d=s).initClass()},function(t,e,i){var n=t(391),r=t(189),P=t(130),o=t(199),j=t(14),s=t(15),a=t(22),N=t(21),_=t(32),l=t(181),p={fill:{},line:{}},d={fill:{fill_alpha:.3,fill_color:\"grey\"},line:{line_alpha:.3,line_color:\"grey\"}},f={fill:{fill_alpha:.2},line:{}},h=function(c){function t(){return null!==c&&c.apply(this,arguments)||this}return n.__extends(t,c),t.prototype.initialize=function(t){c.prototype.initialize.call(this,t);var i=this.model.glyph,n=N.includes(i.mixins,\"fill\"),r=N.includes(i.mixins,\"line\"),o=_.clone(i.attributes);function e(t){var e=_.clone(o);return n&&_.extend(e,t.fill),r&&_.extend(e,t.line),new i.constructor(e)}delete o.id,this.glyph=this.build_glyph_view(i);var s=this.model.selection_glyph;null==s?s=e({fill:{},line:{}}):\"auto\"===s&&(s=e(p)),this.selection_glyph=this.build_glyph_view(s);var a=this.model.nonselection_glyph;null==a?a=e({fill:{},line:{}}):\"auto\"===a&&(a=e(f)),this.nonselection_glyph=this.build_glyph_view(a);var l=this.model.hover_glyph;null!=l&&(this.hover_glyph=this.build_glyph_view(l));var h=this.model.muted_glyph;null!=h&&(this.muted_glyph=this.build_glyph_view(h));var u=e(d);this.decimated_glyph=this.build_glyph_view(u),this.xscale=this.plot_view.frame.xscales[this.model.x_range_name],this.yscale=this.plot_view.frame.yscales[this.model.y_range_name],this.set_data(!1)},t.prototype.build_glyph_view=function(t){return new t.default_view({model:t,renderer:this,plot_view:this.plot_view,parent:this})},t.prototype.connect_signals=function(){var e=this;c.prototype.connect_signals.call(this),this.connect(this.model.change,function(){return e.request_render()}),this.connect(this.model.glyph.change,function(){return e.set_data()}),this.connect(this.model.data_source.change,function(){return e.set_data()}),this.connect(this.model.data_source.streaming,function(){return e.set_data()}),this.connect(this.model.data_source.patching,function(t){return e.set_data(!0,t)}),this.connect(this.model.data_source.selected.change,function(){return e.request_render()}),this.connect(this.model.data_source._select,function(){return e.request_render()}),null!=this.hover_glyph&&this.connect(this.model.data_source.inspect,function(){return e.request_render()}),this.connect(this.model.properties.view.change,function(){return e.set_data()}),this.connect(this.model.view.change,function(){return e.set_data()});var t=this.plot_model.frame,i=t.x_ranges,n=t.y_ranges;for(var r in i){var o=i[r];o instanceof l.FactorRange&&this.connect(o.change,function(){return e.set_data()})}for(var s in n){var o=n[s];o instanceof l.FactorRange&&this.connect(o.change,function(){return e.set_data()})}this.connect(this.model.glyph.transformchange,function(){return e.set_data()})},t.prototype.have_selection_glyphs=function(){return null!=this.selection_glyph&&null!=this.nonselection_glyph},t.prototype.set_data=function(t,e){void 0===t&&(t=!0),void 0===e&&(e=null);var i=Date.now(),n=this.model.data_source;this.all_indices=this.model.view.indices,this.glyph.model.setv({x_range_name:this.model.x_range_name,y_range_name:this.model.y_range_name},{silent:!0}),this.glyph.set_data(n,this.all_indices,e),this.glyph.set_visuals(n),this.decimated_glyph.set_visuals(n),this.have_selection_glyphs()&&(this.selection_glyph.set_visuals(n),this.nonselection_glyph.set_visuals(n)),null!=this.hover_glyph&&this.hover_glyph.set_visuals(n),null!=this.muted_glyph&&this.muted_glyph.set_visuals(n);var r=this.plot_model.plot.lod_factor;this.decimated=[];for(var o=0,s=Math.floor(this.all_indices.length/r);ov?(o=this.decimated,_=this.decimated_glyph,p=this.decimated_glyph):(_=this.model.muted&&null!=this.muted_glyph?this.muted_glyph:this.glyph,p=this.nonselection_glyph),d=this.selection_glyph,null!=this.hover_glyph&&f.length&&(o=N.difference(o,f));var m,g=null;if(l.length&&this.have_selection_glyphs()){for(var y=Date.now(),b={},x=0,w=l;xi?n.slice(-i):n}if(S.isTypedArray(t)){var r=t.length+e.length;if(null!=i&&i=Math.pow(2,i))||e<0||e>=Math.pow(2,i))},t.prototype.parent_by_tile_xyz=function(t,e,i){var n=this.tile_xyz_to_quadkey(t,e,i),r=n.substring(0,n.length-1);return this.quadkey_to_tile_xyz(r)},t.prototype.get_resolution=function(t){return this._computed_initial_resolution()/Math.pow(2,t)},t.prototype.get_resolution_by_extent=function(t,e,i){var n=(t[2]-t[0])/i,r=(t[3]-t[1])/e;return[n,r]},t.prototype.get_level_by_extent=function(t,e,i){for(var n=(t[2]-t[0])/i,r=(t[3]-t[1])/e,o=Math.max(n,r),s=0,a=0,l=this._resolutions;ar.end)&&(this.v_axis_only=!0),(io.end)&&(this.h_axis_only=!0)}null!=this.model.document&&this.model.document.interactive_start(this.plot_model.plot)},e.prototype._pan=function(t){this._update(t.deltaX,t.deltaY),null!=this.model.document&&this.model.document.interactive_start(this.plot_model.plot)},e.prototype._pan_end=function(t){this.h_axis_only=!1,this.v_axis_only=!1,null!=this.pan_info&&this.plot_view.push_state(\"pan\",{range:this.pan_info})},e.prototype._update=function(t,e){var i,n,r,o,s,a,l=this.plot_model.frame,h=t-this.last_dx,u=e-this.last_dy,c=l.bbox.h_range,_=c.start-h,p=c.end-h,d=l.bbox.v_range,f=d.start-u,v=d.end-u,m=this.model.dimensions;\"width\"!=m&&\"both\"!=m||this.v_axis_only?(i=c.start,n=c.end,r=0):(i=_,n=p,r=-h),\"height\"!=m&&\"both\"!=m||this.h_axis_only?(o=d.start,s=d.end,a=0):(o=f,s=v,a=-u),this.last_dx=t,this.last_dy=e;var g=l.xscales,y=l.yscales,b={};for(var x in g){var w=g[x],k=w.r_invert(i,n),S=k[0],C=k[1];b[x]={start:S,end:C}}var T={};for(var A in y){var w=y[A],E=w.r_invert(o,s),S=E[0],C=E[1];T[A]={start:S,end:C}}this.pan_info={xrs:b,yrs:T,sdx:r,sdy:a},this.plot_view.update_range(this.pan_info,!0)},e}(r.GestureToolView);i.PanToolView=s;var a=function(i){function t(t){var e=i.call(this,t)||this;return e.tool_name=\"Pan\",e.event_type=\"pan\",e.default_order=10,e}return n.__extends(t,i),t.initClass=function(){this.prototype.type=\"PanTool\",this.prototype.default_view=s,this.define({dimensions:[o.Dimensions,\"both\"]})},Object.defineProperty(t.prototype,\"tooltip\",{get:function(){return this._get_dim_tooltip(\"Pan\",this.dimensions)},enumerable:!0,configurable:!0}),Object.defineProperty(t.prototype,\"icon\",{get:function(){switch(this.dimensions){case\"both\":return\"bk-tool-icon-pan\";case\"width\":return\"bk-tool-icon-xpan\";case\"height\":return\"bk-tool-icon-ypan\"}},enumerable:!0,configurable:!0}),t}(r.GestureTool);(i.PanTool=a).initClass()},function(t,e,i){var l=t(391),n=t(256),r=t(71),o=t(5),s=t(15),a=t(21),h=function(e){function t(){return null!==e&&e.apply(this,arguments)||this}return l.__extends(t,e),t.prototype.initialize=function(t){e.prototype.initialize.call(this,t),this.data={sx:[],sy:[]}},t.prototype.connect_signals=function(){var t=this;e.prototype.connect_signals.call(this),this.connect(this.model.properties.active.change,function(){return t._active_change()})},t.prototype._active_change=function(){this.model.active||this._clear_data()},t.prototype._keyup=function(t){t.keyCode==o.Keys.Enter&&this._clear_data()},t.prototype._doubletap=function(t){var e=t.shiftKey;this._do_select(this.data.sx,this.data.sy,!0,e),this.plot_view.push_state(\"poly_select\",{selection:this.plot_view.get_selection()}),this._clear_data()},t.prototype._clear_data=function(){this.data={sx:[],sy:[]},this.model.overlay.update({xs:[],ys:[]})},t.prototype._tap=function(t){var e=t.sx,i=t.sy,n=this.plot_model.frame;n.bbox.contains(e,i)&&(this.data.sx.push(e),this.data.sy.push(i),this.model.overlay.update({xs:a.copy(this.data.sx),ys:a.copy(this.data.sy)}))},t.prototype._do_select=function(t,e,i,n){var r={type:\"poly\",sx:t,sy:e};this._select(r,i,n)},t.prototype._emit_callback=function(t){var e=this.computed_renderers[0],i=this.plot_model.frame,n=i.xscales[e.x_range_name],r=i.yscales[e.y_range_name],o=n.v_invert(t.sx),s=r.v_invert(t.sy),a=l.__assign({x:o,y:s},t);this.model.callback.execute(this.model,{geometry:a})},t}(n.SelectToolView);i.PolySelectToolView=h;var u=function(){return new r.PolyAnnotation({level:\"overlay\",xs_units:\"screen\",ys_units:\"screen\",fill_color:{value:\"lightgrey\"},fill_alpha:{value:.5},line_color:{value:\"black\"},line_alpha:{value:1},line_width:{value:2},line_dash:{value:[4,4]}})},c=function(i){function t(t){var e=i.call(this,t)||this;return e.tool_name=\"Poly Select\",e.icon=\"bk-tool-icon-polygon-select\",e.event_type=\"tap\",e.default_order=11,e}return l.__extends(t,i),t.initClass=function(){this.prototype.type=\"PolySelectTool\",this.prototype.default_view=h,this.define({callback:[s.Instance],overlay:[s.Instance,u]})},t}(n.SelectTool);(i.PolySelectTool=c).initClass()},function(t,e,i){var n=t(391),_=t(64),r=t(14),o=t(15),s=t(251);function p(t,e,i,n){if(null==e)return!1;var r=i.compute(e);return Math.abs(t-r)r.right)&&(o=!1)}if(null!=r.bottom&&null!=r.top){var a=n.invert(e);(ar.top)&&(o=!1)}return o}function l(t,e,i,n){var r=e.compute(t),o=e.invert(r+i);return o>=n.start&&o<=n.end?o:t}function h(t,e,i,n){var 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p(t){c[t]?a.setSelectedRows(v.grep(a.getSelectedRows(),function(e){return e!=t})):a.setSelectedRows(a.getSelectedRows().concat(t)),a.setActiveCell(t,function(){if(null===h){h=0;for(var e=a.getColumns(),t=0;t\":\"\":null}v.extend(this,{init:function(e){a=e,n.subscribe(a.onSelectedRowsChanged,t).subscribe(a.onClick,l).subscribe(a.onKeyDown,i),d.hideInFilterHeaderRow||e.onHeaderRowCellRendered.subscribe(function(e,t){\"sel\"===t.column.field&&(v(t.node).empty(),v(\"\").appendTo(t.node).on(\"click\",function(e){f(e,t)}))});d.hideInColumnTitleRow||n.subscribe(a.onHeaderClick,f)},destroy:function(){n.unsubscribeAll()},deSelectRows:function(e){var t,n=e.length,o=[];for(t=0;t\",toolTip:d.toolTip,field:\"sel\",width:d.width,resizable:!1,sortable:!1,cssClass:d.cssClass,hideSelectAllCheckbox:d.hideSelectAllCheckbox,formatter:m}},getOptions:function(){return d},setOptions:function(e){if((d=v.extend(!0,{},d,e)).hideSelectAllCheckbox)o(),r();else if(d.hideInColumnTitleRow?o():(u?a.updateColumnHeader(d.columnId,\"\",d.toolTip):a.updateColumnHeader(d.columnId,\"\",d.toolTip),n.subscribe(a.onHeaderClick,f)),d.hideInFilterHeaderRow)r();else{var t=v(\"#filter-checkbox-selectall-container\");t.show(),t.find('input[type=\"checkbox\"]').prop(\"checked\",u)}}})}}},447:function(e,t,n){var v=e(450),w=e(448);t.exports={RowSelectionModel:function(t){var c,n,o,u=[],r=this,i=new w.EventHandler,l={selectActiveRow:!0};function a(e){return function(){n||(n=!0,e.apply(this,arguments),n=!1)}}function d(e){for(var t=[],n=0;n=this.fromRow&&e<=this.toRow&&t>=this.fromCell&&t<=this.toCell},this.toString=function(){return this.isSingleCell()?\"(\"+this.fromRow+\":\"+this.fromCell+\")\":\"(\"+this.fromRow+\":\"+this.fromCell+\" - \"+this.toRow+\":\"+this.toCell+\")\"}},NonDataRow:o,Group:r,GroupTotals:i,EditorLock:a,GlobalEditorLock:new a,keyCode:{BACKSPACE:8,DELETE:46,DOWN:40,END:35,ENTER:13,ESCAPE:27,ESC:27,HOME:36,INSERT:45,LEFT:37,PAGE_DOWN:34,PAGE_UP:33,RIGHT:39,TAB:9,UP:38,C:67,V:86},preClickClassName:\"slick-edit-preclick\"}},449:function _(require,module,exports){\n", + " /**\n", + " * @license\n", + " * (c) 2009-2016 Michael Leibman\n", + " * michael{dot}leibman{at}gmail{dot}com\n", + " * http://github.com/mleibman/slickgrid\n", + " *\n", + " * Distributed under MIT license.\n", + " * All rights reserved.\n", + " *\n", + " * SlickGrid v2.3\n", + " *\n", + " * NOTES:\n", + " * Cell/row DOM manipulations are done directly bypassing jQuery's DOM manipulation methods.\n", + " * This increases the speed dramatically, but can only be done safely because there are no event handlers\n", + " * or data associated with any cell/row DOM nodes. Cell editors must make sure they implement .destroy()\n", + " * and do proper cleanup.\n", + " */\n", + " var $=require(450),Slick=require(448),scrollbarDimensions,maxSupportedCssHeight;function SlickGrid(container,data,columns,options){$.fn.drag||require(443),$.fn.drop||require(444);var defaults={alwaysShowVerticalScroll:!1,explicitInitialization:!1,rowHeight:25,defaultColumnWidth:80,enableAddRow:!1,leaveSpaceForNewRows:!1,editable:!1,autoEdit:!0,suppressActiveCellChangeOnEdit:!1,enableCellNavigation:!0,enableColumnReorder:!0,asyncEditorLoading:!1,asyncEditorLoadDelay:100,forceFitColumns:!1,enableAsyncPostRender:!1,asyncPostRenderDelay:50,enableAsyncPostRenderCleanup:!1,asyncPostRenderCleanupDelay:40,autoHeight:!1,editorLock:Slick.GlobalEditorLock,showHeaderRow:!1,headerRowHeight:25,createFooterRow:!1,showFooterRow:!1,footerRowHeight:25,createPreHeaderPanel:!1,showPreHeaderPanel:!1,preHeaderPanelHeight:25,showTopPanel:!1,topPanelHeight:25,formatterFactory:null,editorFactory:null,cellFlashingCssClass:\"flashing\",selectedCellCssClass:\"selected\",multiSelect:!0,enableTextSelectionOnCells:!1,dataItemColumnValueExtractor:null,fullWidthRows:!1,multiColumnSort:!1,numberedMultiColumnSort:!1,tristateMultiColumnSort:!1,sortColNumberInSeparateSpan:!1,defaultFormatter:defaultFormatter,forceSyncScrolling:!1,addNewRowCssClass:\"new-row\",preserveCopiedSelectionOnPaste:!1,showCellSelection:!0,viewportClass:null,minRowBuffer:3,emulatePagingWhenScrolling:!0,editorCellNavOnLRKeys:!1},columnDefaults={name:\"\",resizable:!0,sortable:!1,minWidth:30,rerenderOnResize:!1,headerCssClass:null,defaultSortAsc:!0,focusable:!0,selectable:!0},th,h,ph,n,cj,page=0,offset=0,vScrollDir=1,initialized=!1,$container,uid=\"slickgrid_\"+Math.round(1e6*Math.random()),self=this,$focusSink,$focusSink2,$headerScroller,$headers,$headerRow,$headerRowScroller,$headerRowSpacer,$footerRow,$footerRowScroller,$footerRowSpacer,$preHeaderPanel,$preHeaderPanelScroller,$preHeaderPanelSpacer,$topPanelScroller,$topPanel,$viewport,$canvas,$style,$boundAncestors,stylesheet,columnCssRulesL,columnCssRulesR,viewportH,viewportW,canvasWidth,viewportHasHScroll,viewportHasVScroll,headerColumnWidthDiff=0,headerColumnHeightDiff=0,cellWidthDiff=0,cellHeightDiff=0,jQueryNewWidthBehaviour=!1,absoluteColumnMinWidth,tabbingDirection=1,activePosX,activeRow,activeCell,activeCellNode=null,currentEditor=null,serializedEditorValue,editController,rowsCache={},renderedRows=0,numVisibleRows,prevScrollTop=0,scrollTop=0,lastRenderedScrollTop=0,lastRenderedScrollLeft=0,prevScrollLeft=0,scrollLeft=0,selectionModel,selectedRows=[],plugins=[],cellCssClasses={},columnsById={},sortColumns=[],columnPosLeft=[],columnPosRight=[],pagingActive=!1,pagingIsLastPage=!1,scrollThrottle=ActionThrottle(render,50),h_editorLoader=null,h_render=null,h_postrender=null,h_postrenderCleanup=null,postProcessedRows={},postProcessToRow=null,postProcessFromRow=null,postProcessedCleanupQueue=[],postProcessgroupId=0,counter_rows_rendered=0,counter_rows_removed=0,rowNodeFromLastMouseWheelEvent,zombieRowNodeFromLastMouseWheelEvent,zombieRowCacheFromLastMouseWheelEvent,zombieRowPostProcessedFromLastMouseWheelEvent,cssShow={position:\"absolute\",visibility:\"hidden\",display:\"block\"},$hiddenParents,oldProps=[],columnResizeDragging=!1;function init(){if(($container=container instanceof $?container:$(container)).length<1)throw new Error(\"SlickGrid requires a valid container, \"+container+\" does not exist in the DOM.\");cacheCssForHiddenInit(),maxSupportedCssHeight=maxSupportedCssHeight||getMaxSupportedCssHeight(),options=$.extend({},defaults,options),validateAndEnforceOptions(),columnDefaults.width=options.defaultColumnWidth,columnsById={};for(var e=0;et.maxWidth&&(t.width=t.maxWidth)}if(options.enableColumnReorder&&!$.fn.sortable)throw new Error(\"SlickGrid's 'enableColumnReorder = true' option requires jquery-ui.sortable module to be loaded\");editController={commitCurrentEdit:commitCurrentEdit,cancelCurrentEdit:cancelCurrentEdit},$container.empty().css(\"overflow\",\"hidden\").css(\"outline\",0).addClass(uid).addClass(\"ui-widget\"),/relative|absolute|fixed/.test($container.css(\"position\"))||$container.css(\"position\",\"relative\"),$focusSink=$(\"
\").appendTo($container),options.createPreHeaderPanel&&($preHeaderPanelScroller=$(\"
\").appendTo($container),$preHeaderPanel=$(\"
\").appendTo($preHeaderPanelScroller),$preHeaderPanelSpacer=$(\"
\").appendTo($preHeaderPanelScroller),options.showPreHeaderPanel||$preHeaderPanelScroller.hide()),$headerScroller=$(\"
\").appendTo($container),$headers=$(\"
\").appendTo($headerScroller),$headerRowScroller=$(\"
\").appendTo($container),$headerRow=$(\"
\").appendTo($headerRowScroller),$headerRowSpacer=$(\"
\").appendTo($headerRowScroller),$topPanelScroller=$(\"
\").appendTo($container),$topPanel=$(\"
\").appendTo($topPanelScroller),options.showTopPanel||$topPanelScroller.hide(),options.showHeaderRow||$headerRowScroller.hide(),($viewport=$(\"
\").appendTo($container)).css(\"overflow-y\",options.alwaysShowVerticalScroll?\"scroll\":options.autoHeight?\"hidden\":\"auto\"),$viewport.css(\"overflow-x\",options.forceFitColumns?\"hidden\":\"auto\"),options.viewportClass&&$viewport.toggleClass(options.viewportClass,!0),$canvas=$(\"
\").appendTo($viewport),scrollbarDimensions=scrollbarDimensions||measureScrollbar(),$preHeaderPanelSpacer&&$preHeaderPanelSpacer.css(\"width\",getCanvasWidth()+scrollbarDimensions.width+\"px\"),$headers.width(getHeadersWidth()),$headerRowSpacer.css(\"width\",getCanvasWidth()+scrollbarDimensions.width+\"px\"),options.createFooterRow&&($footerRowScroller=$(\"
\").appendTo($container),$footerRow=$(\"
\").appendTo($footerRowScroller),$footerRowSpacer=$(\"
\").css(\"width\",getCanvasWidth()+scrollbarDimensions.width+\"px\").appendTo($footerRowScroller),options.showFooterRow||$footerRowScroller.hide()),$focusSink2=$focusSink.clone().appendTo($container),options.explicitInitialization||finishInitialization()}function finishInitialization(){initialized||(initialized=!0,viewportW=parseFloat($.css($container[0],\"width\",!0)),measureCellPaddingAndBorder(),disableSelection($headers),options.enableTextSelectionOnCells||$viewport.on(\"selectstart.ui\",function(e){return $(e.target).is(\"input,textarea\")}),updateColumnCaches(),createColumnHeaders(),setupColumnSort(),createCssRules(),resizeCanvas(),bindAncestorScrollEvents(),$container.on(\"resize.slickgrid\",resizeCanvas),$viewport.on(\"scroll\",handleScroll),$headerScroller.on(\"contextmenu\",handleHeaderContextMenu).on(\"click\",handleHeaderClick).on(\"mouseenter\",\".slick-header-column\",handleHeaderMouseEnter).on(\"mouseleave\",\".slick-header-column\",handleHeaderMouseLeave),$headerRowScroller.on(\"scroll\",handleHeaderRowScroll),options.createFooterRow&&$footerRowScroller.on(\"scroll\",handleFooterRowScroll),options.createPreHeaderPanel&&$preHeaderPanelScroller.on(\"scroll\",handlePreHeaderPanelScroll),$focusSink.add($focusSink2).on(\"keydown\",handleKeyDown),$canvas.on(\"keydown\",handleKeyDown).on(\"click\",handleClick).on(\"dblclick\",handleDblClick).on(\"contextmenu\",handleContextMenu).on(\"draginit\",handleDragInit).on(\"dragstart\",{distance:3},handleDragStart).on(\"drag\",handleDrag).on(\"dragend\",handleDragEnd).on(\"mouseenter\",\".slick-cell\",handleMouseEnter).on(\"mouseleave\",\".slick-cell\",handleMouseLeave),navigator.userAgent.toLowerCase().match(/webkit/)&&navigator.userAgent.toLowerCase().match(/macintosh/)&&$canvas.on(\"mousewheel\",handleMouseWheel),restoreCssFromHiddenInit())}function cacheCssForHiddenInit(){($hiddenParents=$container.parents().addBack().not(\":visible\")).each(function(){var e={};for(var t in cssShow)e[t]=this.style[t],this.style[t]=cssShow[t];oldProps.push(e)})}function restoreCssFromHiddenInit(){$hiddenParents.each(function(e){var t=oldProps[e];for(var n in cssShow)this.style[n]=t[n]})}function registerPlugin(e){plugins.unshift(e),e.init(self)}function unregisterPlugin(e){for(var t=plugins.length;0<=t;t--)if(plugins[t]===e){plugins[t].destroy&&plugins[t].destroy(),plugins.splice(t,1);break}}function setSelectionModel(e){selectionModel&&(selectionModel.onSelectedRangesChanged.unsubscribe(handleSelectedRangesChanged),selectionModel.destroy&&selectionModel.destroy()),(selectionModel=e)&&(selectionModel.init(self),selectionModel.onSelectedRangesChanged.subscribe(handleSelectedRangesChanged))}function getSelectionModel(){return selectionModel}function getCanvasNode(){return $canvas[0]}function measureScrollbar(){var e=$('
').appendTo($viewport),t=$('
').appendTo(e),n={width:e[0].offsetWidth-e[0].clientWidth,height:e[0].offsetHeight-e[0].clientHeight};return t.remove(),e.remove(),n}function getColumnTotalWidth(e){for(var t=0,n=0,o=columns.length;nviewportW-scrollbarDimensions.width);var n=canvasWidth+(viewportHasVScroll?scrollbarDimensions.width:0);$headerRowSpacer.width(n),options.createFooterRow&&$footerRowSpacer.width(n),options.createPreHeaderPanel&&$preHeaderPanelSpacer.width(n),(canvasWidth!=t||e)&&applyColumnWidths()}function disableSelection(e){e&&e.jquery&&e.attr(\"unselectable\",\"on\").css(\"MozUserSelect\",\"none\").on(\"selectstart.ui\",function(){return!1})}function getMaxSupportedCssHeight(){for(var e=1e6,t=navigator.userAgent.toLowerCase().match(/firefox/)?6e6:1e9,n=$(\"
\").appendTo(document.body);;){var o=2*e;if(n.css(\"height\",o),t\").html(\"\"+o.name+\"\").width(o.width-headerColumnWidthDiff).attr(\"id\",\"\"+uid+o.id).attr(\"title\",o.toolTip||\"\").data(\"column\",o).addClass(o.headerCssClass||\"\").appendTo($headers);if((options.enableColumnReorder||o.sortable)&&r.on(\"mouseenter\",e).on(\"mouseleave\",t),o.sortable&&(r.addClass(\"slick-header-sortable\"),r.append(\"\"),options.numberedMultiColumnSort&&options.sortColNumberInSeparateSpan&&r.append(\"\")),trigger(self.onHeaderCellRendered,{node:r[0],column:o,grid:self}),options.showHeaderRow){var i=$(\"
\").data(\"column\",o).appendTo($headerRow);trigger(self.onHeaderRowCellRendered,{node:i[0],column:o,grid:self})}if(options.createFooterRow&&options.showFooterRow){var l=$(\"
\").data(\"column\",o).appendTo($footerRow);trigger(self.onFooterRowCellRendered,{node:l[0],column:o})}}setSortColumns(sortColumns),setupColumnResize(),options.enableColumnReorder&&(\"function\"==typeof options.enableColumnReorder?options.enableColumnReorder(self,$headers,headerColumnWidthDiff,setColumns,setupColumnResize,columns,getColumnIndex,uid,trigger):setupColumnReorder())}function setupColumnSort(){$headers.click(function(e){if(!columnResizeDragging&&(e.metaKey=e.metaKey||e.ctrlKey,!$(e.target).hasClass(\"slick-resizable-handle\"))){var t=$(e.target).closest(\".slick-header-column\");if(t.length){var n=t.data(\"column\");if(n.sortable){if(!getEditorLock().commitCurrentEdit())return;for(var o=null,r=0;r=columns.length||columns[e].resizable&&(void 0===n&&(n=e),o=e)}),void 0!==n&&u.each(function(l,e){l>=columns.length||l\").appendTo(e).on(\"dragstart\",function(e,t){if(!getEditorLock().commitCurrentEdit())return!1;c=e.pageX,$(this).parent().addClass(\"slick-header-column-active\");var n=null,o=null;if(u.each(function(e,t){e>=columns.length||(columns[e].previousWidth=$(t).outerWidth())}),options.forceFitColumns)for(o=n=0,a=l+1;a
\").appendTo($headers),headerColumnWidthDiff=headerColumnHeightDiff=0,\"border-box\"!=n.css(\"box-sizing\")&&\"border-box\"!=n.css(\"-moz-box-sizing\")&&\"border-box\"!=n.css(\"-webkit-box-sizing\")&&($.each(e,function(e,t){headerColumnWidthDiff+=parseFloat(n.css(t))||0}),$.each(t,function(e,t){headerColumnHeightDiff+=parseFloat(n.css(t))||0})),n.remove();var r=$(\"
\").appendTo($canvas);n=$(\"\").appendTo(r),cellWidthDiff=cellHeightDiff=0,\"border-box\"!=n.css(\"box-sizing\")&&\"border-box\"!=n.css(\"-moz-box-sizing\")&&\"border-box\"!=n.css(\"-webkit-box-sizing\")&&($.each(e,function(e,t){cellWidthDiff+=parseFloat(n.css(t))||0}),$.each(t,function(e,t){cellHeightDiff+=parseFloat(n.css(t))||0})),r.remove(),absoluteColumnMinWidth=Math.max(headerColumnWidthDiff,cellWidthDiff)}function createCssRules(){$style=$(\"\n", + "\n" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "application/javascript": [ + "function HoloViewsWidget() {\n", + "}\n", + "\n", + "HoloViewsWidget.prototype.init_slider = function(init_val){\n", + " if(this.load_json) {\n", + " this.from_json()\n", + " } else {\n", + " this.update_cache();\n", + " }\n", + "}\n", + "\n", + "HoloViewsWidget.prototype.populate_cache = function(idx){\n", + " this.cache[idx].innerHTML = this.frames[idx];\n", + " if (this.embed) {\n", + " delete this.frames[idx];\n", + " }\n", + "}\n", + "\n", + "HoloViewsWidget.prototype.process_error = function(msg){\n", + "}\n", + "\n", + "HoloViewsWidget.prototype.from_json = function() {\n", + " var data_url = this.json_path + this.id + '.json';\n", + " $.getJSON(data_url, $.proxy(function(json_data) {\n", + " this.frames = json_data;\n", + " this.update_cache();\n", + " this.update(0);\n", + " }, this));\n", + "}\n", + "\n", + "HoloViewsWidget.prototype.dynamic_update = function(current){\n", + " if (current === undefined) {\n", + " return\n", + " }\n", + " this.current = current;\n", + " if (this.comm) {\n", + " var msg = {comm_id: this.id+'_client', content: current}\n", + " this.comm.send(msg);\n", + " }\n", + "}\n", + "\n", + "HoloViewsWidget.prototype.update_cache = function(force){\n", + " var frame_len = Object.keys(this.frames).length;\n", + " for (var i=0; i 0) {\n", + " that.time = Date.now();\n", + " that.dynamic_update(that.queue[that.queue.length-1]);\n", + " that.queue = [];\n", + " } else {\n", + " that.wait = false;\n", + " }\n", + " if ((msg.msg_type == \"Ready\") && msg.content) {\n", + " console.log(\"Python callback returned following output:\", msg.content);\n", + " } else if (msg.msg_type == \"Error\") {\n", + " console.log(\"Python failed with the following traceback:\", msg.traceback)\n", + " }\n", + " }\n", + " var comm = HoloViews.comm_manager.get_client_comm(this.plot_id, this.id+'_client', ack_callback);\n", + " return comm\n", + " }\n", + "}\n", + "\n", + "HoloViewsWidget.prototype.msg_handler = function(msg) {\n", + " var metadata = msg.metadata;\n", + " if ((metadata.msg_type == \"Ready\")) {\n", + " if (metadata.content) {\n", + " console.log(\"Python callback returned following output:\", metadata.content);\n", + " }\n", + "\treturn;\n", + " } else if (metadata.msg_type == \"Error\") {\n", + " console.log(\"Python failed with the following traceback:\", metadata.traceback)\n", + " return\n", + " }\n", + " this.process_msg(msg)\n", + "}\n", + "\n", + "HoloViewsWidget.prototype.process_msg = function(msg) {\n", + "}\n", + "\n", + "function SelectionWidget(frames, id, slider_ids, keyMap, dim_vals, notFound, load_json, mode, cached, json_path, dynamic, plot_id){\n", + " this.frames = frames;\n", + " this.id = id;\n", + " this.plot_id = plot_id;\n", + " this.slider_ids = slider_ids;\n", + " this.keyMap = keyMap\n", + " this.current_frame = 0;\n", + " this.current_vals = dim_vals;\n", + " this.load_json = load_json;\n", + " this.mode = mode;\n", + " this.notFound = notFound;\n", + " this.cached = cached;\n", + " this.dynamic = dynamic;\n", + " this.cache = {};\n", + " this.json_path = json_path;\n", + " this.init_slider(this.current_vals[0]);\n", + " this.queue = [];\n", + " this.wait = false;\n", + " if (!this.cached || this.dynamic) {\n", + " this.comm = this.init_comms();\n", + " }\n", + "}\n", + "\n", + "SelectionWidget.prototype = new HoloViewsWidget;\n", + "\n", + "\n", + "SelectionWidget.prototype.get_key = function(current_vals) {\n", + " var key = \"(\";\n", + " for (var i=0; i Date.now()))) {\n", + " this.queue.push(key);\n", + " return\n", + " }\n", + " this.queue = [];\n", + " this.time = Date.now();\n", + " this.current_frame = key;\n", + " this.wait = true;\n", + " this.dynamic_update(key)\n", + " } else if (key !== undefined) {\n", + " this.update(key)\n", + " }\n", + "}\n", + "\n", + "\n", + "/* Define the ScrubberWidget class */\n", + "function ScrubberWidget(frames, num_frames, id, interval, load_json, mode, cached, json_path, dynamic, plot_id){\n", + " this.slider_id = \"_anim_slider\" + id;\n", + " this.loop_select_id = \"_anim_loop_select\" + id;\n", + " this.id = id;\n", + " this.plot_id = plot_id;\n", + " this.interval = interval;\n", + " this.current_frame = 0;\n", + " this.direction = 0;\n", + " this.dynamic = dynamic;\n", + " this.timer = null;\n", + " this.load_json = load_json;\n", + " this.mode = mode;\n", + " this.cached = cached;\n", + " this.frames = frames;\n", + " this.cache = {};\n", + " this.length = num_frames;\n", + " this.json_path = json_path;\n", + " document.getElementById(this.slider_id).max = this.length - 1;\n", + " this.init_slider(0);\n", + " this.wait = false;\n", + " this.queue = [];\n", + " if (!this.cached || this.dynamic) {\n", + " this.comm = this.init_comms()\n", + " }\n", + "}\n", + "\n", + "ScrubberWidget.prototype = new HoloViewsWidget;\n", + "\n", + "ScrubberWidget.prototype.set_frame = function(frame){\n", + " this.current_frame = frame;\n", + " var widget = document.getElementById(this.slider_id);\n", + " if (widget === null) {\n", + " this.pause_animation();\n", + " return\n", + " }\n", + " widget.value = this.current_frame;\n", + " if (this.dynamic || !this.cached) {\n", + " if ((this.time !== undefined) && ((this.wait) && ((this.time + 10000) > Date.now()))) {\n", + " this.queue.push(frame);\n", + " return\n", + " }\n", + " this.queue = [];\n", + " this.time = Date.now();\n", + " this.wait = true;\n", + " this.dynamic_update(frame)\n", + " } else {\n", + " this.update(frame)\n", + " }\n", + "}\n", + "\n", + "ScrubberWidget.prototype.get_loop_state = function(){\n", + " var button_group = document[this.loop_select_id].state;\n", + " for (var i = 0; i < button_group.length; i++) {\n", + " var button = button_group[i];\n", + " if (button.checked) {\n", + " return button.value;\n", + " }\n", + " }\n", + " return undefined;\n", + "}\n", + "\n", + "\n", + "ScrubberWidget.prototype.next_frame = function() {\n", + " this.set_frame(Math.min(this.length - 1, this.current_frame + 1));\n", + "}\n", + "\n", + "ScrubberWidget.prototype.previous_frame = function() {\n", + " this.set_frame(Math.max(0, this.current_frame - 1));\n", + "}\n", + "\n", + "ScrubberWidget.prototype.first_frame = function() {\n", + " this.set_frame(0);\n", + "}\n", + "\n", + "ScrubberWidget.prototype.last_frame = function() {\n", + " this.set_frame(this.length - 1);\n", + "}\n", + "\n", + "ScrubberWidget.prototype.slower = function() {\n", + " this.interval /= 0.7;\n", + " if(this.direction > 0){this.play_animation();}\n", + " else if(this.direction < 0){this.reverse_animation();}\n", + "}\n", + "\n", + "ScrubberWidget.prototype.faster = function() {\n", + " this.interval *= 0.7;\n", + " if(this.direction > 0){this.play_animation();}\n", + " else if(this.direction < 0){this.reverse_animation();}\n", + "}\n", + "\n", + "ScrubberWidget.prototype.anim_step_forward = function() {\n", + " if(this.current_frame < this.length - 1){\n", + " this.next_frame();\n", + " }else{\n", + " var loop_state = this.get_loop_state();\n", + " if(loop_state == \"loop\"){\n", + " this.first_frame();\n", + " }else if(loop_state == \"reflect\"){\n", + " this.last_frame();\n", + " this.reverse_animation();\n", + " }else{\n", + " this.pause_animation();\n", + " this.last_frame();\n", + " }\n", + " }\n", + "}\n", + "\n", + "ScrubberWidget.prototype.anim_step_reverse = function() {\n", + " if(this.current_frame > 0){\n", + " this.previous_frame();\n", + " } else {\n", + " var loop_state = this.get_loop_state();\n", + " if(loop_state == \"loop\"){\n", + " this.last_frame();\n", + " }else if(loop_state == \"reflect\"){\n", + " this.first_frame();\n", + " this.play_animation();\n", + " }else{\n", + " this.pause_animation();\n", + " this.first_frame();\n", + " }\n", + " }\n", + "}\n", + "\n", + "ScrubberWidget.prototype.pause_animation = function() {\n", + " this.direction = 0;\n", + " if (this.timer){\n", + " clearInterval(this.timer);\n", + " this.timer = null;\n", + " }\n", + "}\n", + "\n", + "ScrubberWidget.prototype.play_animation = function() {\n", + " this.pause_animation();\n", + " this.direction = 1;\n", + " var t = this;\n", + " if (!this.timer) this.timer = setInterval(function(){t.anim_step_forward();}, this.interval);\n", + "}\n", + "\n", + "ScrubberWidget.prototype.reverse_animation = function() {\n", + " this.pause_animation();\n", + " this.direction = -1;\n", + " var t = this;\n", + " if (!this.timer) this.timer = setInterval(function(){t.anim_step_reverse();}, this.interval);\n", + "}\n", + "\n", + "function extend(destination, source) {\n", + " for (var k in source) {\n", + " if (source.hasOwnProperty(k)) {\n", + " destination[k] = source[k];\n", + " }\n", + " }\n", + " return destination;\n", + "}\n", + "\n", + "function update_widget(widget, values) {\n", + " if (widget.hasClass(\"ui-slider\")) {\n", + " widget.slider('option', {\n", + " min: 0,\n", + " max: values.length-1,\n", + " dim_vals: values,\n", + " value: 0,\n", + " dim_labels: values\n", + " })\n", + " widget.slider('option', 'slide').call(widget, event, {value: 0})\n", + " } else {\n", + " widget.empty();\n", + " for (var i=0; i\", {\n", + " value: i,\n", + " text: values[i]\n", + " }))\n", + " };\n", + " widget.data('values', values);\n", + " widget.data('value', 0);\n", + " widget.trigger(\"change\");\n", + " };\n", + "}\n", + "\n", + "function init_slider(id, plot_id, dim, values, next_vals, labels, dynamic, step, value, next_dim,\n", + " dim_idx, delay, jQueryUI_CDN, UNDERSCORE_CDN) {\n", + " // Slider JS Block START\n", + " function loadcssfile(filename){\n", + " var fileref=document.createElement(\"link\")\n", + " fileref.setAttribute(\"rel\", \"stylesheet\")\n", + " fileref.setAttribute(\"type\", \"text/css\")\n", + " fileref.setAttribute(\"href\", filename)\n", + " document.getElementsByTagName(\"head\")[0].appendChild(fileref)\n", + " }\n", + " loadcssfile(\"https://code.jquery.com/ui/1.10.4/themes/smoothness/jquery-ui.css\");\n", + " /* Check if jQuery and jQueryUI have been loaded\n", + " otherwise load with require.js */\n", + " var jQuery = window.jQuery,\n", + " // check for old versions of jQuery\n", + " oldjQuery = jQuery && !!jQuery.fn.jquery.match(/^1\\.[0-4](\\.|$)/),\n", + " jquery_path = '',\n", + " paths = {},\n", + " noConflict;\n", + " var jQueryUI = jQuery.ui;\n", + " // check for jQuery\n", + " if (!jQuery || oldjQuery) {\n", + " // load if it's not available or doesn't meet min standards\n", + " paths.jQuery = jQuery;\n", + " noConflict = !!oldjQuery;\n", + " } else {\n", + " // register the current jQuery\n", + " define('jquery', [], function() { return jQuery; });\n", + " }\n", + " if (!jQueryUI) {\n", + " paths.jQueryUI = jQueryUI_CDN.slice(null, -3);\n", + " } else {\n", + " define('jQueryUI', [], function() { return jQuery.ui; });\n", + " }\n", + " paths.underscore = UNDERSCORE_CDN.slice(null, -3);\n", + " var jquery_require = {\n", + " paths: paths,\n", + " shim: {\n", + " \"jQueryUI\": {\n", + " exports:\"$\",\n", + " deps: ['jquery']\n", + " },\n", + " \"underscore\": {\n", + " exports: '_'\n", + " }\n", + " }\n", + " }\n", + " require.config(jquery_require);\n", + " require([\"jQueryUI\", \"underscore\"], function(jUI, _){\n", + " if (noConflict) $.noConflict(true);\n", + " var vals = values;\n", + " if (dynamic && vals.constructor === Array) {\n", + " var default_value = parseFloat(value);\n", + " var min = parseFloat(vals[0]);\n", + " var max = parseFloat(vals[vals.length-1]);\n", + " var wstep = step;\n", + " var wlabels = [default_value];\n", + " var init_label = default_value;\n", + " } else {\n", + " var min = 0;\n", + " if (dynamic) {\n", + " var max = Object.keys(vals).length - 1;\n", + " var init_label = labels[value];\n", + " var default_value = values[value];\n", + " } else {\n", + " var max = vals.length - 1;\n", + " var init_label = labels[value];\n", + " var default_value = value;\n", + " }\n", + " var wstep = 1;\n", + " var wlabels = labels;\n", + " }\n", + " function adjustFontSize(text) {\n", + " var width_ratio = (text.parent().width()/8)/text.val().length;\n", + " var size = Math.min(0.9, Math.max(0.6, width_ratio))+'em';\n", + " text.css('font-size', size);\n", + " }\n", + " var slider = $('#_anim_widget'+id+'_'+dim);\n", + " slider.slider({\n", + " animate: \"fast\",\n", + " min: min,\n", + " max: max,\n", + " step: wstep,\n", + " value: default_value,\n", + " dim_vals: vals,\n", + " dim_labels: wlabels,\n", + " next_vals: next_vals,\n", + " slide: function(event, ui) {\n", + " var vals = slider.slider(\"option\", \"dim_vals\");\n", + " var next_vals = slider.slider(\"option\", \"next_vals\");\n", + " var dlabels = slider.slider(\"option\", \"dim_labels\");\n", + " if (dynamic) {\n", + " var dim_val = ui.value;\n", + " if (vals.constructor === Array) {\n", + " var label = ui.value;\n", + " } else {\n", + " var label = dlabels[ui.value];\n", + " }\n", + " } else {\n", + " var dim_val = vals[ui.value];\n", + " var label = dlabels[ui.value];\n", + " }\n", + " var text = $('#textInput'+id+'_'+dim);\n", + " text.val(label);\n", + " adjustFontSize(text);\n", + " HoloViews.index[plot_id].set_frame(dim_val, dim_idx);\n", + " if (Object.keys(next_vals).length > 0) {\n", + " var new_vals = next_vals[dim_val];\n", + " var next_widget = $('#_anim_widget'+id+'_'+next_dim);\n", + " update_widget(next_widget, new_vals);\n", + " }\n", + " }\n", + " });\n", + " slider.keypress(function(event) {\n", + " if (event.which == 80 || event.which == 112) {\n", + " var start = slider.slider(\"option\", \"value\");\n", + " var stop = slider.slider(\"option\", \"max\");\n", + " for (var i=start; i<=stop; i++) {\n", + " var delay = i*delay;\n", + " $.proxy(function doSetTimeout(i) { setTimeout($.proxy(function() {\n", + " var val = {value:i};\n", + " slider.slider('value',i);\n", + " slider.slider(\"option\", \"slide\")(null, val);\n", + " }, slider), delay);}, slider)(i);\n", + " }\n", + " }\n", + " if (event.which == 82 || event.which == 114) {\n", + " var start = slider.slider(\"option\", \"value\");\n", + " var stop = slider.slider(\"option\", \"min\");\n", + " var count = 0;\n", + " for (var i=start; i>=stop; i--) {\n", + " var delay = count*delay;\n", + " count = count + 1;\n", + " $.proxy(function doSetTimeout(i) { setTimeout($.proxy(function() {\n", + " var val = {value:i};\n", + " slider.slider('value',i);\n", + " slider.slider(\"option\", \"slide\")(null, val);\n", + " }, slider), delay);}, slider)(i);\n", + " }\n", + " }\n", + " });\n", + " var textInput = $('#textInput'+id+'_'+dim)\n", + " textInput.val(init_label);\n", + " adjustFontSize(textInput);\n", + " });\n", + "}\n", + "\n", + "function init_dropdown(id, plot_id, dim, vals, value, next_vals, labels, next_dim, dim_idx, dynamic) {\n", + " var widget = $(\"#_anim_widget\"+id+'_'+dim);\n", + " widget.data('values', vals)\n", + " for (var i=0; i\", {\n", + " value: val,\n", + " text: labels[i]\n", + " }));\n", + " };\n", + " widget.data(\"next_vals\", next_vals);\n", + " widget.val(value);\n", + " widget.on('change', function(event, ui) {\n", + " if (dynamic) {\n", + " var dim_val = parseInt(this.value);\n", + " } else {\n", + " var dim_val = $.data(this, 'values')[this.value];\n", + " }\n", + " var next_vals = $.data(this, \"next_vals\");\n", + " if (Object.keys(next_vals).length > 0) {\n", + " var new_vals = next_vals[dim_val];\n", + " var next_widget = $('#_anim_widget'+id+'_'+next_dim);\n", + " update_widget(next_widget, new_vals);\n", + " }\n", + " var widgets = HoloViews.index[plot_id]\n", + " if (widgets) {\n", + " widgets.set_frame(dim_val, dim_idx);\n", + " }\n", + " });\n", + "}\n", + "\n", + "\n", + "if (window.HoloViews === undefined) {\n", + " window.HoloViews = {}\n", + " window.PyViz = window.HoloViews\n", + "} else if (window.PyViz === undefined) {\n", + " window.PyViz = window.HoloViews\n", + "}\n", + "\n", + "\n", + "var _namespace = {\n", + " init_slider: init_slider,\n", + " init_dropdown: init_dropdown,\n", + " comms: {},\n", + " comm_status: {},\n", + " index: {},\n", + " plot_index: {},\n", + " kernels: {},\n", + " receivers: {}\n", + "}\n", + "\n", + "for (var k in _namespace) {\n", + " if (!(k in window.HoloViews)) {\n", + " window.HoloViews[k] = _namespace[k];\n", + " }\n", + "}\n", + "\n", + "// Define Bokeh specific subclasses\n", + "function BokehSelectionWidget() {\n", + " SelectionWidget.apply(this, arguments);\n", + "}\n", + "\n", + "function BokehScrubberWidget() {\n", + " ScrubberWidget.apply(this, arguments);\n", + "}\n", + "\n", + "// Let them inherit from the baseclasses\n", + "BokehSelectionWidget.prototype = Object.create(SelectionWidget.prototype);\n", + "BokehScrubberWidget.prototype = Object.create(ScrubberWidget.prototype);\n", + "\n", + "// Define methods to override on widgets\n", + "var BokehMethods = {\n", + " update_cache : function(){\n", + " for (var index in this.frames) {\n", + " this.frames[index] = JSON.parse(this.frames[index]);\n", + " }\n", + " },\n", + " update : function(current){\n", + " if (current === undefined) {\n", + " return;\n", + " }\n", + " var data = this.frames[current];\n", + " if (data !== undefined) {\n", + " if (data.root in HoloViews.plot_index) {\n", + " var doc = HoloViews.plot_index[data.root].model.document;\n", + " } else {\n", + " var doc = Bokeh.index[data.root].model.document;\n", + " }\n", + " doc.apply_json_patch(data.content);\n", + " }\n", + " },\n", + " init_comms: function() {\n", + " if (Bokeh.protocol !== undefined) {\n", + " this.receiver = new Bokeh.protocol.Receiver()\n", + " } else {\n", + " this.receiver = null;\n", + " }\n", + " return HoloViewsWidget.prototype.init_comms.call(this);\n", + " },\n", + " process_msg : function(msg) {\n", + " if (this.plot_id in HoloViews.plot_index) {\n", + " var doc = HoloViews.plot_index[this.plot_id].model.document;\n", + " } else {\n", + " var doc = Bokeh.index[this.plot_id].model.document;\n", + " }\n", + " if (this.receiver === null) { return }\n", + " var receiver = this.receiver;\n", + " if (msg.buffers.length > 0) {\n", + " receiver.consume(msg.buffers[0].buffer)\n", + " } else {\n", + " receiver.consume(msg.content.data)\n", + " }\n", + " const comm_msg = receiver.message;\n", + " if ((comm_msg != null) && (doc != null)) {\n", + " doc.apply_json_patch(comm_msg.content, comm_msg.buffers)\n", + " }\n", + " }\n", + "}\n", + "\n", + "// Extend Bokeh widgets with backend specific methods\n", + "extend(BokehSelectionWidget.prototype, BokehMethods);\n", + "extend(BokehScrubberWidget.prototype, BokehMethods);\n", + "\n", + "window.HoloViews.BokehSelectionWidget = BokehSelectionWidget\n", + "window.HoloViews.BokehScrubberWidget = BokehScrubberWidget\n", + "\n", + " function JupyterCommManager() {\n", + " }\n", + "\n", + " JupyterCommManager.prototype.register_target = function(plot_id, comm_id, msg_handler) {\n", + " if (window.comm_manager || ((window.Jupyter !== undefined) && (Jupyter.notebook.kernel != null))) {\n", + " var comm_manager = window.comm_manager || Jupyter.notebook.kernel.comm_manager;\n", + " comm_manager.register_target(comm_id, function(comm) {\n", + " comm.on_msg(msg_handler);\n", + " });\n", + " } else if ((plot_id in window.PyViz.kernels) && (window.PyViz.kernels[plot_id])) {\n", + " window.PyViz.kernels[plot_id].registerCommTarget(comm_id, function(comm) {\n", + " comm.onMsg = msg_handler;\n", + " });\n", + " }\n", + " }\n", + "\n", + " JupyterCommManager.prototype.get_client_comm = function(plot_id, comm_id, msg_handler) {\n", + " if (comm_id in window.PyViz.comms) {\n", + " return window.PyViz.comms[comm_id];\n", + " } else if (window.comm_manager || ((window.Jupyter !== undefined) && (Jupyter.notebook.kernel != null))) {\n", + " var comm_manager = window.comm_manager || Jupyter.notebook.kernel.comm_manager;\n", + " var comm = comm_manager.new_comm(comm_id, {}, {}, {}, comm_id);\n", + " if (msg_handler) {\n", + " comm.on_msg(msg_handler);\n", + " }\n", + " } else if ((plot_id in window.PyViz.kernels) && (window.PyViz.kernels[plot_id])) {\n", + " var comm = window.PyViz.kernels[plot_id].connectToComm(comm_id);\n", + " comm.open();\n", + " if (msg_handler) {\n", + " comm.onMsg = msg_handler;\n", + " }\n", + " }\n", + "\n", + " window.PyViz.comms[comm_id] = comm;\n", + " return comm;\n", + " }\n", + "\n", + " window.PyViz.comm_manager = new JupyterCommManager();\n", + " \n", + "\n", + "var JS_MIME_TYPE = 'application/javascript';\n", + "var HTML_MIME_TYPE = 'text/html';\n", + "var EXEC_MIME_TYPE = 'application/vnd.holoviews_exec.v0+json';\n", + "var CLASS_NAME = 'output';\n", + "\n", + "/**\n", + " * Render data to the DOM node\n", + " */\n", + "function render(props, node) {\n", + " var div = document.createElement(\"div\");\n", + " var script = document.createElement(\"script\");\n", + " node.appendChild(div);\n", + " node.appendChild(script);\n", + "}\n", + "\n", + "/**\n", + " * Handle when a new output is added\n", + " */\n", + "function handle_add_output(event, handle) {\n", + " var output_area = handle.output_area;\n", + " var output = handle.output;\n", + " if ((output.data == undefined) || (!output.data.hasOwnProperty(EXEC_MIME_TYPE))) {\n", + " return\n", + " }\n", + " var id = output.metadata[EXEC_MIME_TYPE][\"id\"];\n", + " var toinsert = output_area.element.find(\".\" + CLASS_NAME.split(' ')[0]);\n", + " if (id !== undefined) {\n", + " var nchildren = toinsert.length;\n", + " toinsert[nchildren-1].children[0].innerHTML = output.data[HTML_MIME_TYPE];\n", + " toinsert[nchildren-1].children[1].textContent = output.data[JS_MIME_TYPE];\n", + " output_area._hv_plot_id = id;\n", + " if ((window.Bokeh !== undefined) && (id in Bokeh.index)) {\n", + " window.PyViz.plot_index[id] = Bokeh.index[id];\n", + " } else {\n", + " window.PyViz.plot_index[id] = null;\n", + " }\n", + " }\n", + "}\n", + "\n", + "/**\n", + " * Handle when an output is cleared or removed\n", + " */\n", + "function handle_clear_output(event, handle) {\n", + " var id = handle.cell.output_area._hv_plot_id;\n", + " if ((id === undefined) || !(id in PyViz.plot_index)) { return; }\n", + " var comm = window.PyViz.comm_manager.get_client_comm(\"hv-extension-comm\", \"hv-extension-comm\", function () {});\n", + " if (comm !== null) {\n", + " comm.send({event_type: 'delete', 'id': id});\n", + " }\n", + " delete PyViz.plot_index[id];\n", + " if ((window.Bokeh !== undefined) & (id in window.Bokeh.index)) {\n", + " var doc = window.Bokeh.index[id].model.document\n", + " doc.clear();\n", + " const i = window.Bokeh.documents.indexOf(doc);\n", + " if (i > -1) {\n", + " window.Bokeh.documents.splice(i, 1);\n", + " }\n", + " }\n", + "}\n", + "\n", + "/**\n", + " * Handle kernel restart event\n", + " */\n", + "function handle_kernel_cleanup(event, handle) {\n", + " delete PyViz.comms[\"hv-extension-comm\"];\n", + " window.PyViz.plot_index = {}\n", + "}\n", + "\n", + "/**\n", + " * Handle update_display_data messages\n", + " */\n", + "function handle_update_output(event, handle) {\n", + " handle_clear_output(event, {cell: {output_area: handle.output_area}})\n", + " handle_add_output(event, handle)\n", + "}\n", + "\n", + "function register_renderer(events, OutputArea) {\n", + " function append_mime(data, metadata, element) {\n", + " // create a DOM node to render to\n", + " var toinsert = this.create_output_subarea(\n", + " metadata,\n", + " CLASS_NAME,\n", + " EXEC_MIME_TYPE\n", + " );\n", + " this.keyboard_manager.register_events(toinsert);\n", + " // Render to node\n", + " var props = {data: data, metadata: metadata[EXEC_MIME_TYPE]};\n", + " render(props, toinsert[0]);\n", + " element.append(toinsert);\n", + " return toinsert\n", + " }\n", + "\n", + " events.on('output_added.OutputArea', handle_add_output);\n", + " events.on('output_updated.OutputArea', handle_update_output);\n", + " events.on('clear_output.CodeCell', handle_clear_output);\n", + " events.on('delete.Cell', handle_clear_output);\n", + " events.on('kernel_ready.Kernel', handle_kernel_cleanup);\n", + "\n", + " OutputArea.prototype.register_mime_type(EXEC_MIME_TYPE, append_mime, {\n", + " safe: true,\n", + " index: 0\n", + " });\n", + "}\n", + "\n", + "if (window.Jupyter !== undefined) {\n", + " try {\n", + " var events = require('base/js/events');\n", + " var OutputArea = require('notebook/js/outputarea').OutputArea;\n", + " if (OutputArea.prototype.mime_types().indexOf(EXEC_MIME_TYPE) == -1) {\n", + " register_renderer(events, OutputArea);\n", + " }\n", + " } catch(err) {\n", + " }\n", + "}\n" + ], + "application/vnd.holoviews_load.v0+json": "function HoloViewsWidget() {\n}\n\nHoloViewsWidget.prototype.init_slider = function(init_val){\n if(this.load_json) {\n this.from_json()\n } else {\n this.update_cache();\n }\n}\n\nHoloViewsWidget.prototype.populate_cache = function(idx){\n this.cache[idx].innerHTML = this.frames[idx];\n if (this.embed) {\n delete this.frames[idx];\n }\n}\n\nHoloViewsWidget.prototype.process_error = function(msg){\n}\n\nHoloViewsWidget.prototype.from_json = function() {\n var data_url = this.json_path + this.id + '.json';\n $.getJSON(data_url, $.proxy(function(json_data) {\n this.frames = json_data;\n this.update_cache();\n this.update(0);\n }, this));\n}\n\nHoloViewsWidget.prototype.dynamic_update = function(current){\n if (current === undefined) {\n return\n }\n this.current = current;\n if (this.comm) {\n var msg = {comm_id: this.id+'_client', content: current}\n this.comm.send(msg);\n }\n}\n\nHoloViewsWidget.prototype.update_cache = function(force){\n var frame_len = Object.keys(this.frames).length;\n for (var i=0; i 0) {\n that.time = Date.now();\n that.dynamic_update(that.queue[that.queue.length-1]);\n that.queue = [];\n } else {\n that.wait = false;\n }\n if ((msg.msg_type == \"Ready\") && msg.content) {\n console.log(\"Python callback returned following output:\", msg.content);\n } else if (msg.msg_type == \"Error\") {\n console.log(\"Python failed with the following traceback:\", msg.traceback)\n }\n }\n var comm = HoloViews.comm_manager.get_client_comm(this.plot_id, this.id+'_client', ack_callback);\n return comm\n }\n}\n\nHoloViewsWidget.prototype.msg_handler = function(msg) {\n var metadata = msg.metadata;\n if ((metadata.msg_type == \"Ready\")) {\n if (metadata.content) {\n console.log(\"Python callback returned following output:\", metadata.content);\n }\n\treturn;\n } else if (metadata.msg_type == \"Error\") {\n console.log(\"Python failed with the following traceback:\", metadata.traceback)\n return\n }\n this.process_msg(msg)\n}\n\nHoloViewsWidget.prototype.process_msg = function(msg) {\n}\n\nfunction SelectionWidget(frames, id, slider_ids, keyMap, dim_vals, notFound, load_json, mode, cached, json_path, dynamic, plot_id){\n this.frames = frames;\n this.id = id;\n this.plot_id = plot_id;\n this.slider_ids = slider_ids;\n this.keyMap = keyMap\n this.current_frame = 0;\n this.current_vals = dim_vals;\n this.load_json = load_json;\n this.mode = mode;\n this.notFound = notFound;\n this.cached = cached;\n this.dynamic = dynamic;\n this.cache = {};\n this.json_path = json_path;\n this.init_slider(this.current_vals[0]);\n this.queue = [];\n this.wait = false;\n if (!this.cached || this.dynamic) {\n this.comm = this.init_comms();\n }\n}\n\nSelectionWidget.prototype = new HoloViewsWidget;\n\n\nSelectionWidget.prototype.get_key = function(current_vals) {\n var key = \"(\";\n for (var i=0; i Date.now()))) {\n this.queue.push(key);\n return\n }\n this.queue = [];\n this.time = Date.now();\n this.current_frame = key;\n this.wait = true;\n this.dynamic_update(key)\n } else if (key !== undefined) {\n this.update(key)\n }\n}\n\n\n/* Define the ScrubberWidget class */\nfunction ScrubberWidget(frames, num_frames, id, interval, load_json, mode, cached, json_path, dynamic, plot_id){\n this.slider_id = \"_anim_slider\" + id;\n this.loop_select_id = \"_anim_loop_select\" + id;\n this.id = id;\n this.plot_id = plot_id;\n this.interval = interval;\n this.current_frame = 0;\n this.direction = 0;\n this.dynamic = dynamic;\n this.timer = null;\n this.load_json = load_json;\n this.mode = mode;\n this.cached = cached;\n this.frames = frames;\n this.cache = {};\n this.length = num_frames;\n this.json_path = json_path;\n document.getElementById(this.slider_id).max = this.length - 1;\n this.init_slider(0);\n this.wait = false;\n this.queue = [];\n if (!this.cached || this.dynamic) {\n this.comm = this.init_comms()\n }\n}\n\nScrubberWidget.prototype = new HoloViewsWidget;\n\nScrubberWidget.prototype.set_frame = function(frame){\n this.current_frame = frame;\n var widget = document.getElementById(this.slider_id);\n if (widget === null) {\n this.pause_animation();\n return\n }\n widget.value = this.current_frame;\n if (this.dynamic || !this.cached) {\n if ((this.time !== undefined) && ((this.wait) && ((this.time + 10000) > Date.now()))) {\n this.queue.push(frame);\n return\n }\n this.queue = [];\n this.time = Date.now();\n this.wait = true;\n this.dynamic_update(frame)\n } else {\n this.update(frame)\n }\n}\n\nScrubberWidget.prototype.get_loop_state = function(){\n var button_group = document[this.loop_select_id].state;\n for (var i = 0; i < button_group.length; i++) {\n var button = button_group[i];\n if (button.checked) {\n return button.value;\n }\n }\n return undefined;\n}\n\n\nScrubberWidget.prototype.next_frame = function() {\n this.set_frame(Math.min(this.length - 1, this.current_frame + 1));\n}\n\nScrubberWidget.prototype.previous_frame = function() {\n this.set_frame(Math.max(0, this.current_frame - 1));\n}\n\nScrubberWidget.prototype.first_frame = function() {\n this.set_frame(0);\n}\n\nScrubberWidget.prototype.last_frame = function() {\n this.set_frame(this.length - 1);\n}\n\nScrubberWidget.prototype.slower = function() {\n this.interval /= 0.7;\n if(this.direction > 0){this.play_animation();}\n else if(this.direction < 0){this.reverse_animation();}\n}\n\nScrubberWidget.prototype.faster = function() {\n this.interval *= 0.7;\n if(this.direction > 0){this.play_animation();}\n else if(this.direction < 0){this.reverse_animation();}\n}\n\nScrubberWidget.prototype.anim_step_forward = function() {\n if(this.current_frame < this.length - 1){\n this.next_frame();\n }else{\n var loop_state = this.get_loop_state();\n if(loop_state == \"loop\"){\n this.first_frame();\n }else if(loop_state == \"reflect\"){\n this.last_frame();\n this.reverse_animation();\n }else{\n this.pause_animation();\n this.last_frame();\n }\n }\n}\n\nScrubberWidget.prototype.anim_step_reverse = function() {\n if(this.current_frame > 0){\n this.previous_frame();\n } else {\n var loop_state = this.get_loop_state();\n if(loop_state == \"loop\"){\n this.last_frame();\n }else if(loop_state == \"reflect\"){\n this.first_frame();\n this.play_animation();\n }else{\n this.pause_animation();\n this.first_frame();\n }\n }\n}\n\nScrubberWidget.prototype.pause_animation = function() {\n this.direction = 0;\n if (this.timer){\n clearInterval(this.timer);\n this.timer = null;\n }\n}\n\nScrubberWidget.prototype.play_animation = function() {\n this.pause_animation();\n this.direction = 1;\n var t = this;\n if (!this.timer) this.timer = setInterval(function(){t.anim_step_forward();}, this.interval);\n}\n\nScrubberWidget.prototype.reverse_animation = function() {\n this.pause_animation();\n this.direction = -1;\n var t = this;\n if (!this.timer) this.timer = setInterval(function(){t.anim_step_reverse();}, this.interval);\n}\n\nfunction extend(destination, source) {\n for (var k in source) {\n if (source.hasOwnProperty(k)) {\n destination[k] = source[k];\n }\n }\n return destination;\n}\n\nfunction update_widget(widget, values) {\n if (widget.hasClass(\"ui-slider\")) {\n widget.slider('option', {\n min: 0,\n max: values.length-1,\n dim_vals: values,\n value: 0,\n dim_labels: values\n })\n widget.slider('option', 'slide').call(widget, event, {value: 0})\n } else {\n widget.empty();\n for (var i=0; i\", {\n value: i,\n text: values[i]\n }))\n };\n widget.data('values', values);\n widget.data('value', 0);\n widget.trigger(\"change\");\n };\n}\n\nfunction init_slider(id, plot_id, dim, values, next_vals, labels, dynamic, step, value, next_dim,\n dim_idx, delay, jQueryUI_CDN, UNDERSCORE_CDN) {\n // Slider JS Block START\n function loadcssfile(filename){\n var fileref=document.createElement(\"link\")\n fileref.setAttribute(\"rel\", \"stylesheet\")\n fileref.setAttribute(\"type\", \"text/css\")\n fileref.setAttribute(\"href\", filename)\n document.getElementsByTagName(\"head\")[0].appendChild(fileref)\n }\n loadcssfile(\"https://code.jquery.com/ui/1.10.4/themes/smoothness/jquery-ui.css\");\n /* Check if jQuery and jQueryUI have been loaded\n otherwise load with require.js */\n var jQuery = window.jQuery,\n // check for old versions of jQuery\n oldjQuery = jQuery && !!jQuery.fn.jquery.match(/^1\\.[0-4](\\.|$)/),\n jquery_path = '',\n paths = {},\n noConflict;\n var jQueryUI = jQuery.ui;\n // check for jQuery\n if (!jQuery || oldjQuery) {\n // load if it's not available or doesn't meet min standards\n paths.jQuery = jQuery;\n noConflict = !!oldjQuery;\n } else {\n // register the current jQuery\n define('jquery', [], function() { return jQuery; });\n }\n if (!jQueryUI) {\n paths.jQueryUI = jQueryUI_CDN.slice(null, -3);\n } else {\n define('jQueryUI', [], function() { return jQuery.ui; });\n }\n paths.underscore = UNDERSCORE_CDN.slice(null, -3);\n var jquery_require = {\n paths: paths,\n shim: {\n \"jQueryUI\": {\n exports:\"$\",\n deps: ['jquery']\n },\n \"underscore\": {\n exports: '_'\n }\n }\n }\n require.config(jquery_require);\n require([\"jQueryUI\", \"underscore\"], function(jUI, _){\n if (noConflict) $.noConflict(true);\n var vals = values;\n if (dynamic && vals.constructor === Array) {\n var default_value = parseFloat(value);\n var min = parseFloat(vals[0]);\n var max = parseFloat(vals[vals.length-1]);\n var wstep = step;\n var wlabels = [default_value];\n var init_label = default_value;\n } else {\n var min = 0;\n if (dynamic) {\n var max = Object.keys(vals).length - 1;\n var init_label = labels[value];\n var default_value = values[value];\n } else {\n var max = vals.length - 1;\n var init_label = labels[value];\n var default_value = value;\n }\n var wstep = 1;\n var wlabels = labels;\n }\n function adjustFontSize(text) {\n var width_ratio = (text.parent().width()/8)/text.val().length;\n var size = Math.min(0.9, Math.max(0.6, width_ratio))+'em';\n text.css('font-size', size);\n }\n var slider = $('#_anim_widget'+id+'_'+dim);\n slider.slider({\n animate: \"fast\",\n min: min,\n max: max,\n step: wstep,\n value: default_value,\n dim_vals: vals,\n dim_labels: wlabels,\n next_vals: next_vals,\n slide: function(event, ui) {\n var vals = slider.slider(\"option\", \"dim_vals\");\n var next_vals = slider.slider(\"option\", \"next_vals\");\n var dlabels = slider.slider(\"option\", \"dim_labels\");\n if (dynamic) {\n var dim_val = ui.value;\n if (vals.constructor === Array) {\n var label = ui.value;\n } else {\n var label = dlabels[ui.value];\n }\n } else {\n var dim_val = vals[ui.value];\n var label = dlabels[ui.value];\n }\n var text = $('#textInput'+id+'_'+dim);\n text.val(label);\n adjustFontSize(text);\n HoloViews.index[plot_id].set_frame(dim_val, dim_idx);\n if (Object.keys(next_vals).length > 0) {\n var new_vals = next_vals[dim_val];\n var next_widget = $('#_anim_widget'+id+'_'+next_dim);\n update_widget(next_widget, new_vals);\n }\n }\n });\n slider.keypress(function(event) {\n if (event.which == 80 || event.which == 112) {\n var start = slider.slider(\"option\", \"value\");\n var stop = slider.slider(\"option\", \"max\");\n for (var i=start; i<=stop; i++) {\n var delay = i*delay;\n $.proxy(function doSetTimeout(i) { setTimeout($.proxy(function() {\n var val = {value:i};\n slider.slider('value',i);\n slider.slider(\"option\", \"slide\")(null, val);\n }, slider), delay);}, slider)(i);\n }\n }\n if (event.which == 82 || event.which == 114) {\n var start = slider.slider(\"option\", \"value\");\n var stop = slider.slider(\"option\", \"min\");\n var count = 0;\n for (var i=start; i>=stop; i--) {\n var delay = count*delay;\n count = count + 1;\n $.proxy(function doSetTimeout(i) { setTimeout($.proxy(function() {\n var val = {value:i};\n slider.slider('value',i);\n slider.slider(\"option\", \"slide\")(null, val);\n }, slider), delay);}, slider)(i);\n }\n }\n });\n var textInput = $('#textInput'+id+'_'+dim)\n textInput.val(init_label);\n adjustFontSize(textInput);\n });\n}\n\nfunction init_dropdown(id, plot_id, dim, vals, value, next_vals, labels, next_dim, dim_idx, dynamic) {\n var widget = $(\"#_anim_widget\"+id+'_'+dim);\n widget.data('values', vals)\n for (var i=0; i\", {\n value: val,\n text: labels[i]\n }));\n };\n widget.data(\"next_vals\", next_vals);\n widget.val(value);\n widget.on('change', function(event, ui) {\n if (dynamic) {\n var dim_val = parseInt(this.value);\n } else {\n var dim_val = $.data(this, 'values')[this.value];\n }\n var next_vals = $.data(this, \"next_vals\");\n if (Object.keys(next_vals).length > 0) {\n var new_vals = next_vals[dim_val];\n var next_widget = $('#_anim_widget'+id+'_'+next_dim);\n update_widget(next_widget, new_vals);\n }\n var widgets = HoloViews.index[plot_id]\n if (widgets) {\n widgets.set_frame(dim_val, dim_idx);\n }\n });\n}\n\n\nif (window.HoloViews === undefined) {\n window.HoloViews = {}\n window.PyViz = window.HoloViews\n} else if (window.PyViz === undefined) {\n window.PyViz = window.HoloViews\n}\n\n\nvar _namespace = {\n init_slider: init_slider,\n init_dropdown: init_dropdown,\n comms: {},\n comm_status: {},\n index: {},\n plot_index: {},\n kernels: {},\n receivers: {}\n}\n\nfor (var k in _namespace) {\n if (!(k in window.HoloViews)) {\n window.HoloViews[k] = _namespace[k];\n }\n}\n\n// Define Bokeh specific subclasses\nfunction BokehSelectionWidget() {\n SelectionWidget.apply(this, arguments);\n}\n\nfunction BokehScrubberWidget() {\n ScrubberWidget.apply(this, arguments);\n}\n\n// Let them inherit from the baseclasses\nBokehSelectionWidget.prototype = Object.create(SelectionWidget.prototype);\nBokehScrubberWidget.prototype = Object.create(ScrubberWidget.prototype);\n\n// Define methods to override on widgets\nvar BokehMethods = {\n update_cache : function(){\n for (var index in this.frames) {\n this.frames[index] = JSON.parse(this.frames[index]);\n }\n },\n update : function(current){\n if (current === undefined) {\n return;\n }\n var data = this.frames[current];\n if (data !== undefined) {\n if (data.root in HoloViews.plot_index) {\n var doc = HoloViews.plot_index[data.root].model.document;\n } else {\n var doc = Bokeh.index[data.root].model.document;\n }\n doc.apply_json_patch(data.content);\n }\n },\n init_comms: function() {\n if (Bokeh.protocol !== undefined) {\n this.receiver = new Bokeh.protocol.Receiver()\n } else {\n this.receiver = null;\n }\n return HoloViewsWidget.prototype.init_comms.call(this);\n },\n process_msg : function(msg) {\n if (this.plot_id in HoloViews.plot_index) {\n var doc = HoloViews.plot_index[this.plot_id].model.document;\n } else {\n var doc = Bokeh.index[this.plot_id].model.document;\n }\n if (this.receiver === null) { return }\n var receiver = this.receiver;\n if (msg.buffers.length > 0) {\n receiver.consume(msg.buffers[0].buffer)\n } else {\n receiver.consume(msg.content.data)\n }\n const comm_msg = receiver.message;\n if ((comm_msg != null) && (doc != null)) {\n doc.apply_json_patch(comm_msg.content, comm_msg.buffers)\n }\n }\n}\n\n// Extend Bokeh widgets with backend specific methods\nextend(BokehSelectionWidget.prototype, BokehMethods);\nextend(BokehScrubberWidget.prototype, BokehMethods);\n\nwindow.HoloViews.BokehSelectionWidget = BokehSelectionWidget\nwindow.HoloViews.BokehScrubberWidget = BokehScrubberWidget\n\n function JupyterCommManager() {\n }\n\n JupyterCommManager.prototype.register_target = function(plot_id, comm_id, msg_handler) {\n if (window.comm_manager || ((window.Jupyter !== undefined) && (Jupyter.notebook.kernel != null))) {\n var comm_manager = window.comm_manager || Jupyter.notebook.kernel.comm_manager;\n comm_manager.register_target(comm_id, function(comm) {\n comm.on_msg(msg_handler);\n });\n } else if ((plot_id in window.PyViz.kernels) && (window.PyViz.kernels[plot_id])) {\n window.PyViz.kernels[plot_id].registerCommTarget(comm_id, function(comm) {\n comm.onMsg = msg_handler;\n });\n }\n }\n\n JupyterCommManager.prototype.get_client_comm = function(plot_id, comm_id, msg_handler) {\n if (comm_id in window.PyViz.comms) {\n return window.PyViz.comms[comm_id];\n } else if (window.comm_manager || ((window.Jupyter !== undefined) && (Jupyter.notebook.kernel != null))) {\n var comm_manager = window.comm_manager || Jupyter.notebook.kernel.comm_manager;\n var comm = comm_manager.new_comm(comm_id, {}, {}, {}, comm_id);\n if (msg_handler) {\n comm.on_msg(msg_handler);\n }\n } else if ((plot_id in window.PyViz.kernels) && (window.PyViz.kernels[plot_id])) {\n var comm = window.PyViz.kernels[plot_id].connectToComm(comm_id);\n comm.open();\n if (msg_handler) {\n comm.onMsg = msg_handler;\n }\n }\n\n window.PyViz.comms[comm_id] = comm;\n return comm;\n }\n\n window.PyViz.comm_manager = new JupyterCommManager();\n \n\nvar JS_MIME_TYPE = 'application/javascript';\nvar HTML_MIME_TYPE = 'text/html';\nvar EXEC_MIME_TYPE = 'application/vnd.holoviews_exec.v0+json';\nvar CLASS_NAME = 'output';\n\n/**\n * Render data to the DOM node\n */\nfunction render(props, node) {\n var div = document.createElement(\"div\");\n var script = document.createElement(\"script\");\n node.appendChild(div);\n node.appendChild(script);\n}\n\n/**\n * Handle when a new output is added\n */\nfunction handle_add_output(event, handle) {\n var output_area = handle.output_area;\n var output = handle.output;\n if ((output.data == undefined) || (!output.data.hasOwnProperty(EXEC_MIME_TYPE))) {\n return\n }\n var id = output.metadata[EXEC_MIME_TYPE][\"id\"];\n var toinsert = output_area.element.find(\".\" + CLASS_NAME.split(' ')[0]);\n if (id !== undefined) {\n var nchildren = toinsert.length;\n toinsert[nchildren-1].children[0].innerHTML = output.data[HTML_MIME_TYPE];\n toinsert[nchildren-1].children[1].textContent = output.data[JS_MIME_TYPE];\n output_area._hv_plot_id = id;\n if ((window.Bokeh !== undefined) && (id in Bokeh.index)) {\n window.PyViz.plot_index[id] = Bokeh.index[id];\n } else {\n window.PyViz.plot_index[id] = null;\n }\n }\n}\n\n/**\n * Handle when an output is cleared or removed\n */\nfunction handle_clear_output(event, handle) {\n var id = handle.cell.output_area._hv_plot_id;\n if ((id === undefined) || !(id in PyViz.plot_index)) { return; }\n var comm = window.PyViz.comm_manager.get_client_comm(\"hv-extension-comm\", \"hv-extension-comm\", function () {});\n if (comm !== null) {\n comm.send({event_type: 'delete', 'id': id});\n }\n delete PyViz.plot_index[id];\n if ((window.Bokeh !== undefined) & (id in window.Bokeh.index)) {\n var doc = window.Bokeh.index[id].model.document\n doc.clear();\n const i = window.Bokeh.documents.indexOf(doc);\n if (i > -1) {\n window.Bokeh.documents.splice(i, 1);\n }\n }\n}\n\n/**\n * Handle kernel restart event\n */\nfunction handle_kernel_cleanup(event, handle) {\n delete PyViz.comms[\"hv-extension-comm\"];\n window.PyViz.plot_index = {}\n}\n\n/**\n * Handle update_display_data messages\n */\nfunction handle_update_output(event, handle) {\n handle_clear_output(event, {cell: {output_area: handle.output_area}})\n handle_add_output(event, handle)\n}\n\nfunction register_renderer(events, OutputArea) {\n function append_mime(data, metadata, element) {\n // create a DOM node to render to\n var toinsert = this.create_output_subarea(\n metadata,\n CLASS_NAME,\n EXEC_MIME_TYPE\n );\n this.keyboard_manager.register_events(toinsert);\n // Render to node\n var props = {data: data, metadata: metadata[EXEC_MIME_TYPE]};\n render(props, toinsert[0]);\n element.append(toinsert);\n return toinsert\n }\n\n events.on('output_added.OutputArea', handle_add_output);\n events.on('output_updated.OutputArea', handle_update_output);\n events.on('clear_output.CodeCell', handle_clear_output);\n events.on('delete.Cell', handle_clear_output);\n events.on('kernel_ready.Kernel', handle_kernel_cleanup);\n\n OutputArea.prototype.register_mime_type(EXEC_MIME_TYPE, append_mime, {\n safe: true,\n index: 0\n });\n}\n\nif (window.Jupyter !== undefined) {\n try {\n var events = require('base/js/events');\n var OutputArea = require('notebook/js/outputarea').OutputArea;\n if (OutputArea.prototype.mime_types().indexOf(EXEC_MIME_TYPE) == -1) {\n register_renderer(events, OutputArea);\n }\n } catch(err) {\n }\n}\n" + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "scanpy==1.4+223.gc5cec58 anndata==0.6.19+4.g473413a numpy==1.16.2 scipy==1.2.1 pandas==0.24.2 scikit-learn==0.20.3 statsmodels==0.9.0 python-igraph==0.7.1 louvain==0.6.1 \n" + ] + } + ], + "source": [ + "import scanpy as sc\n", + "\n", + "import seaborn as sns\n", + "\n", + "sc.logging.print_versions()" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [], + "source": [ + "from pathlib import Path\n", + "\n", + "DATAPTH = Path(\"./data/pbmc_1k_v3_filtered_feature_bc_matrix.h5\")\n", + "CACHEDIR = Path(\"./cache\")\n", + "\n", + "if not DATAPTH.parent.is_dir():\n", + " DATAPTH.parent.mkdir()\n", + "if not DATAPTH.is_file():\n", + " !wget -O {DATAPTH} http://cf.10xgenomics.com/samples/cell-exp/3.0.0/pbmc_1k_v3/pbmc_1k_v3_filtered_feature_bc_matrix.h5" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Variable names are not unique. To make them unique, call `.var_names_make_unique`.\n", + "Variable names are not unique. To make them unique, call `.var_names_make_unique`.\n", + "Variable names are not unique. To make them unique, call `.var_names_make_unique`.\n" + ] + } + ], + "source": [ + "pbmcs = sc.read_10x_h5(\"./data/pbmc_1k_v3_filtered_feature_bc_matrix.h5\")\n", + "\n", + "# Making var names unique\n", + "pbmcs.var[\"gene_symbols\"] = pbmcs.var.index\n", + "pbmcs.var.set_index(\"gene_ids\", inplace=True)\n", + "\n", + "# Filtering out boring var columns\n", + "boring_cols = pbmcs.var.apply(lambda x: len(x.unique()) == 1)\n", + "pbmcs.var.drop(pbmcs.var.columns[boring_cols], axis=1, inplace=True)" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "AnnData object with n_obs × n_vars = 1222 × 33538 \n", + " var: 'gene_symbols'" + ] + }, + "execution_count": 4, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "pbmcs" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## QC metrics" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Now we'll calculate some qc metrics." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "# Mark mitochondrial genes\n", + "pbmcs.var[\"mito\"] = pbmcs.var[\"gene_symbols\"].str.startswith(\"MT-\")\n", + "\n", + "# Calculate qc metrics, can be slow for first run\n", + "sc.pp.calculate_qc_metrics(pbmcs, qc_vars=[\"mito\"], inplace=True)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "pbmcs" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Static QC plots" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Lets start taking a look at some of these metrics. We'll start with using `seaborn`. `seaborn` gives you access to a number of useful statistical plots for tidy data, which both the `obs` and `var` annotation dataframes are.\n", + "\n", + "To start, lets look at a single variable, the proportion of each cells expression that was from mitochondrial content:" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "sns.distplot(pbmcs.obs[\"pct_counts_mito\"])" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Clearly, there're outliers we'd like to filter out. Now lets look at the relationship between total counts and unique genes per cell:" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "sns.jointplot(\n", + " x=\"log1p_n_genes_by_counts\", y=\"log1p_total_counts\", data=pbmcs.obs, kind=\"hex\"\n", + ")" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "
\n", + "\n", + "**Note**\n", + " \n", + "These plots have a lot of options, and I'd highly recommend checking out the docs. Some common variants I use are log density to see outliers better, and alternate color schemes. Here are some example you can try:\n", + "\n", + "```python\n", + "import matplotlib as mpl\n", + "\n", + "# Log density\n", + "sns.jointplot(\n", + " x=\"log1p_n_genes_by_counts\", y=\"log1p_total_counts\", data=pbmcs.obs, kind=\"hex\",\n", + " norm=mpl.colors.LogNorm()\n", + ")\n", + "\n", + "# Alternate color scheme\n", + "sns.jointplot(\n", + " x=\"log1p_n_genes_by_counts\", y=\"log1p_total_counts\", data=pbmcs.obs, kind=\"hex\",\n", + " cmap=sns.cubehelix_palette(light=1, dark=0.1, as_cmap=True, reverse=True)\n", + ")\n", + "```\n", + "\n", + "
" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Interactive QC plots" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Similar plots can be made interactive (hover over) with `hvplot`:" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "pbmcs.obs.hvplot.scatter(\n", + " \"log1p_n_genes_by_counts\", \"log1p_total_counts\", width=500, height=400\n", + ")" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "pbmcs.obs.hvplot.hist(\"pct_counts_mito\")" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "pbmcs.obs.hvplot.hist(\"total_counts\")" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Filtering" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Based on our QC plots, we'll filter" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "pbmcs = pbmcs[pbmcs.obs[\"pct_counts_mito\"] < 30, :]\n", + "pbmcs = pbmcs[pbmcs.obs[\"log1p_n_genes_by_counts\"] > 6.5, :]\n", + "pbmcs = pbmcs[pbmcs.obs[\"log1p_total_counts\"] > 8, :].copy()\n", + "\n", + "sc.pp.filter_genes(pbmcs, min_counts=1) # Remove genes with no counts" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "pbmcs" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "pbmcs.write(CACHEDIR / \"pbmcs_1k_v3_filtered.h5ad\", compression=\"gzip\")" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "pbmcs = sc.read(CACHEDIR / \"pbmcs_1k_v3_filtered.h5ad\")" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Normalize and cluster:\n", + "\n", + "Here we'll just go through typical normalization and clustering for a single cell dataset:" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "# Normalize\n", + "sc.pp.normalize_per_cell(pbmcs, counts_per_cell_after=1000)\n", + "sc.pp.log1p(pbmcs)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "# Dim reduce\n", + "sc.pp.pca(pbmcs)\n", + "sc.pp.neighbors(pbmcs, n_neighbors=30)\n", + "sc.tl.umap(pbmcs)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "# Cluster\n", + "sc.tl.leiden(pbmcs, resolution=0.8)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Visualizing using `scanpy`'s plotting tools:" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "sc.pl.umap(pbmcs, color=[\"leiden\"], legend_loc=\"on data\")\n", + "sc.pl.umap(\n", + " pbmcs,\n", + " color=[\"CST3\", \"NKG7\", \"IL7R\", \"MS4A1\"],\n", + " gene_symbols=\"gene_symbols\",\n", + " use_raw=False,\n", + ") # Some markers for quick validation" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Interactive volcano plots:" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Now I'll demonstrate how we can look at differential expression to figure out what's different between groups `2` and `4` using `hvplot`." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "import pandas as pd\n", + "\n", + "\n", + "def rank_genes_groups_df(\n", + " adata,\n", + " group: str,\n", + " pval_cutoff: float = 0.05,\n", + " logfc_cutoff: float = None,\n", + " gene_symbols: str = None,\n", + "):\n", + " \"\"\"Turn results of `rank_genes_groups` into a dataframe.\"\"\"\n", + " d = pd.DataFrame()\n", + " for k in [\"scores\", \"names\", \"logfoldchanges\", \"pvals\", \"pvals_adj\"]:\n", + " d[k] = adata.uns[\"rank_genes_groups\"][k][group]\n", + " if pval_cutoff is not None:\n", + " d = d[d[\"pvals_adj\"] < pval_cutoff]\n", + " if logfc_cutoff is not None:\n", + " d = d[d[\"logfoldchanges\"].abs() > logfc_cutoff]\n", + " if gene_symbols is not None:\n", + " d = d.join(pbmcs.var[gene_symbols], on=\"names\")\n", + " return d" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "sc.tl.rank_genes_groups(\n", + " pbmcs, groupby=\"leiden\", groups=[\"2\"], reference=\"4\", n_genes=pbmcs.shape[1]\n", + ")\n", + "de_df = rank_genes_groups_df(pbmcs, \"2\", gene_symbols=\"gene_symbols\")" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "de_df.head(10)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "# Simple interactive volcano plot with hover over\n", + "de_df.hvplot.scatter(\n", + " \"logfoldchanges\",\n", + " \"pvals_adj\",\n", + " flip_yaxis=True,\n", + " logy=True,\n", + " hover_cols=[\"gene_symbols\", \"names\"], # Adds variable to be shown in hover over\n", + " size=10,\n", + " padding=(0.05, 0.05),\n", + ")" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "But we can go beyond hover-over. You'll have to be actually running the notebook for this one to work. Try selecting some points with the lasso tool in the next plot, then running the following cell:" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "from holoviews.streams import Selection1D\n", + "\n", + "volcano = de_df.hvplot.scatter(\n", + " \"logfoldchanges\",\n", + " \"pvals_adj\",\n", + " flip_yaxis=True,\n", + " logy=True,\n", + " hover_cols=[\"gene_symbols\", \"names\"], # Adds variable to be shown in hover over\n", + " size=10,\n", + " padding=(0.05, 0.05),\n", + " tools=[\"lasso_select\"],\n", + ")\n", + "\n", + "sel = Selection1D(source=volcano)\n", + "\n", + "volcano" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "de_df.iloc[sel.index][\"gene_symbols\"]" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python3", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.7.2" + }, + "toc": { + "colors": { + "hover_highlight": "#DAA520", + "navigate_num": "#000000", + "navigate_text": "#333333", + "running_highlight": "#FF0000", + "selected_highlight": "#FFD700", + "sidebar_border": "#EEEEEE", + "wrapper_background": "#FFFFFF" + }, + "moveMenuLeft": true, + "nav_menu": { + "height": "174px", + "width": "252px" + }, + "navigate_menu": true, + "number_sections": false, + "sideBar": false, + "threshold": 4, + "toc_cell": false, + "toc_section_display": "block", + "toc_window_display": false, + "widenNotebook": false + } + }, + "nbformat": 4, + "nbformat_minor": 2 +}