celldega 0.6.0 → 0.6.1

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Files changed (2) hide show
  1. package/package.json +1 -1
  2. package/src/celldega/static/widget.js +1 -1
package/package.json CHANGED
@@ -1,6 +1,6 @@
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  {
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  "name": "celldega",
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- "version": "0.6.0",
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+ "version": "0.6.1",
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  "type": "module",
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  "scripts": {
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  "dev": "npm run build -- --sourcemap=inline --watch",
package/src/celldega/static/widget.js CHANGED
@@ -1722,7 +1722,7 @@ ${g.stack}`:B}var LE=0,nM=new TextEncoder("utf-8"),_eA=typeof nM.encodeInto=="fu
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  if(bool(picking.isActive)){
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  widthPixels.xy += pickingLineWidthExtraPixels;
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  }
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- `),{...A,inject:{...A.inject||{},"vs:#decl":(A.inject?.["vs:#decl"]||"").concat("uniform float pickingLineWidthExtraPixels;")}}}draw(A){super.draw({...A,uniforms:{...A.uniforms,pickingLineWidthExtraPixels:this.props.pickingLineWidthExtraPixels}})}};Vn.defaultProps=AnA;Vn.layerName="EditablePathLayer";var gnA=[0,0,0,153],InA=[0,0,0,144],BnA=[0,0,0,255],QnA=[0,0,144,144],CnA=[144,144,144,255],EnA=[144,144,144,144],inA=[192,0,0,255],onA=[0,0,0,128],tnA=[124,0,192,255],enA=[255,255,255,255],anA=5,DnA=3,snA=7,rnA=32*X0,gV=HE;function rt(g){return!g||typeof g!="function"?g:A=>g(nnA(A))}function nnA(g){return g.__source?g.__source.object:g.sourceFeature?g.sourceFeature.feature:g}function AV(g){switch(g.properties.editHandleType){case"existing":return inA;case"snap-source":return tnA;case"intermediate":default:return onA}}function cnA(g){return enA}function GnA(g){switch(g.properties.editHandleType){case"existing":return anA;case"snap":return snA;case"intermediate":default:return DnA}}var wnA={mode:gV,onEdit:()=>{},pickable:!0,pickingRadius:10,pickingDepth:5,fp64:!1,filled:!0,stroked:!0,lineWidthScale:X0,lineWidthMinPixels:1,lineWidthMaxPixels:Number.MAX_SAFE_INTEGER,pickingLineWidthExtraPixels:0,lineWidthUnits:"pixels",lineJointRounded:!1,lineCapRounded:!1,lineMiterLimit:4,pointRadiusScale:1,pointRadiusMinPixels:2,pointRadiusMaxPixels:Number.MAX_SAFE_INTEGER,getLineColor:(g,A,I)=>A?BnA:gnA,getFillColor:(g,A,I)=>A?QnA:InA,getRadius:g=>g&&g.properties&&g.properties.radius||g&&g.properties&&g.properties.size||1,getLineWidth:g=>g&&g.properties&&g.properties.lineWidth||3,getTentativeLineColor:g=>CnA,getTentativeFillColor:g=>EnA,getTentativeLineWidth:g=>g&&g.properties&&g.properties.lineWidth||3,editHandleType:"point",editHandlePointRadiusScale:1,editHandlePointOutline:!0,editHandlePointStrokeWidth:2,editHandlePointRadiusUnits:"pixels",editHandlePointRadiusMinPixels:4,editHandlePointRadiusMaxPixels:8,getEditHandlePointColor:AV,getEditHandlePointOutlineColor:cnA,getEditHandlePointRadius:GnA,editHandleIconAtlas:null,editHandleIconMapping:null,editHandleIconSizeScale:1,editHandleIconSizeUnits:"pixels",getEditHandleIcon:g=>g.properties.editHandleType,getEditHandleIconSize:10,getEditHandleIconColor:AV,getEditHandleIconAngle:0,billboard:!0},hnA={view:pC,modify:Go,translate:new Pn(new at),transform:new Pn(new j0),scale:Ue,rotate:Se,duplicate:M0,split:q0,extrude:d0,elevation:U0,drawPoint:S0,drawLineString:L0,drawPolygon:HE,drawRectangle:Ms,drawSquare:f0,drawRectangleFromCenter:u0,drawSquareFromCenter:m0,drawCircleFromCenter:b0,drawCircleByBoundingBox:T0,drawEllipseByBoundingBox:W0,drawRectangleUsing3Points:Z0,drawEllipseUsing3Points:P0,draw90DegreePolygon:O0,drawPolygonByDragging:V0},nt=class extends On{constructor(){super(...arguments);p(this,"state")}renderLayers(){let I=this.getSubLayerProps({id:"geojson",data:this.props.data,fp64:this.props.fp64,filled:this.props.filled,stroked:this.props.stroked,lineWidthScale:this.props.lineWidthScale,lineWidthMinPixels:this.props.lineWidthMinPixels,lineWidthMaxPixels:this.props.lineWidthMaxPixels,lineWidthUnits:this.props.lineWidthUnits,lineJointRounded:this.props.lineJointRounded,lineCapRounded:this.props.lineCapRounded,lineMiterLimit:this.props.lineMiterLimit,pointRadiusScale:this.props.pointRadiusScale,pointRadiusMinPixels:this.props.pointRadiusMinPixels,pointRadiusMaxPixels:this.props.pointRadiusMaxPixels,getLineColor:this.selectionAwareAccessor(this.props.getLineColor),getFillColor:this.selectionAwareAccessor(this.props.getFillColor),getPointRadius:this.selectionAwareAccessor(this.props.getRadius),getLineWidth:this.selectionAwareAccessor(this.props.getLineWidth),_subLayerProps:{linestrings:{billboard:this.props.billboard,updateTriggers:{all:[this.props.selectedFeatureIndexes,this.props.mode]}},"polygons-stroke":{billboard:this.props.billboard,pickingLineWidthExtraPixels:this.props.pickingLineWidthExtraPixels,type:Vn,updateTriggers:{all:[this.props.selectedFeatureIndexes,this.props.mode]}}},updateTriggers:{getLineColor:[this.props.selectedFeatureIndexes,this.props.mode],getFillColor:[this.props.selectedFeatureIndexes,this.props.mode],getPointRadius:[this.props.selectedFeatureIndexes,this.props.mode],getLineWidth:[this.props.selectedFeatureIndexes,this.props.mode]}}),B=[new Xt(I)];return B=B.concat(this.createGuidesLayers(),this.createTooltipsLayers()),B}initializeState(){super.initializeState(),this.setState({selectedFeatures:[],editHandles:[]})}shouldUpdateState(I){return super.shouldUpdateState(I)||I.changeFlags.stateChanged}updateState({props:I,oldProps:B,changeFlags:Q,context:C}){if(super.updateState({oldProps:B,props:I,changeFlags:Q,context:C}),Q.propsOrDataChanged&&(Object.keys(B).length===0||I.mode!==B.mode)){let e;if(typeof I.mode=="function"){let D=I.mode;e=new D}else typeof I.mode=="string"?(e=hnA[I.mode],console.warn("Deprecated use of passing `mode` as a string. 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w.nbhd.alpha_nbhd=!1,w.nbhd.ini_feature_collection={type:"FeatureCollection",features:[],inst_alpha:null},w.nbhd.feature_collection=w.nbhd.ini_feature_collection;w.containers={},w.custom_callbacks={},w.custom_callbacks.view_change=G,w.cats={},w.cats.cat,w.cats.reset_cat=!1,w.cats.selected_cats=[],w.cats.cell_cats=[],w.cats.dict_cell_cats={},w.cats.color_dict_cluster={},w.cats.cluster_counts=[],w.cats.polygon_cell_names=[],w.cats.svg_bar_cluster=Ve("svg"),w.genes={},w.genes.color_dict_gene={},w.genes.gene_names=[],w.genes.meta_gene={},w.genes.gene_counts=[],w.genes.selected_genes=[],w.genes.trx_ini_radius=D,w.genes.trx_names_array=[],w.genes.trx_data=[],w.genes.gene_text_box="",w.genes.trx_slider=document.createElement("input"),w.genes.gene_search=document.createElement("div"),w.genes.svg_bar_gene=Ve("svg"),w.cats.cell_exp_array=[],w.cats.cell_names_array=[],w.cats.cell_name_to_index_map=new Map,w.img={},w.img.image_layer_colors={},w.img.image_layer_sliders={},LN(I);let k="dapi";await fN(w.img,o);let F=w.img.landscape_parameters.image_info;MV(w.img,w.img.landscape_parameters.image_format),lV(w.img,F),U8(w.img),JV(w.img.image_layer_colors,w.img.image_info);let h=document.createElement("div");h.style.height=n+"px",h.style.border="1px solid #d3d3d3",await uN(w,o,k),await Vl(w.genes,o),await KV(w),w.views=Pl();let y=await NV(h,r,n);RV(y,B,Q,C,E),kV(y,w.views),w.cache={},w.cache.cell=await AL(),w.cache.trx=await AL(),w.combo_data={},w.tooltip_cat_cell="",yV(y,w),w.edit={},w.edit.svg_bar_rgn=Ve("svg"),w.edit.rgn_areas=[],w.edit.color_dict_rgn={},w.edit.rgn_opacity=.75,w.edit.visible=!1,w.edit.modify_index=null,Object.keys(w.model).length!==0?Object.keys(w.model.get("region")).length===0?w.edit.feature_collection={type:"FeatureCollection",features:[]}:w.edit.feature_collection=w.model.get("region"):w.edit.feature_collection={type:"FeatureCollection",features:[]};let J=l8(w),M=await F8(w),l=await nV(o,w),Y=await DV(w),U=p8(w.genes),x=IV(w),q=CV(w,!1),W={background_layer:J,image_layers:M,cell_layer:l,path_layer:Y,trx_layer:U,edit_layer:x,nbhd_layer:q};cV(y,W,w),rV(y,W,w),q8(y,W,w),BV(y,W,w),QV(y,W,w),EV(y,W,w),UM(W,D);let P=Qg(W,w.close_up);y.setProps({layers:P}),FV(y,W,w),Object.keys(w.model).length>0&&(w.model.on("change:update_trigger",()=>pV(y,W,w)),w.model.on("change:cell_clusters",()=>qV(y,W,w)));let v=aV(e,y,W,w);return g.appendChild(v),g.appendChild(h),{update_matrix_gene:async X=>{let L=X===w.cats.cat,aA=L?"cluster":X;if(L)w.containers.bar_gene.scrollTo({top:0,behavior:"smooth"});else{let yA=w.genes.svg_bar_gene.selectAll("g").filter(function(){let RA=qA(this).select("text").node();return RA&&RA.textContent===X}).attr("opacity",1);if(!yA.empty()){let RA=yA.node().getBoundingClientRect().top,UA=w.containers.bar_gene.getBoundingClientRect().top,$=RA-UA+w.containers.bar_gene.scrollTop;w.genes.svg_bar_gene.attr("opacity",1),w.containers.bar_gene.scrollTo({top:$,behavior:"smooth"})}}w.cats.svg_bar_cluster.selectAll("g").attr("font-weight","normal").attr("opacity",1),iB(W,w,w.cats.cat===X),ug(w.cats,aA),HI(w.genes,[X]),Vg(w.cats,[]),await to(w.cats,w.genes,w.global_base_url,X),fI(W,aA),$I(W,aA),GB(w.genes,W);let wA=Qg(W,w.close_up);y.setProps({layers:wA}),w.genes.gene_search_input.value=w.genes.gene_search_input.value!==X?X:"",RQ(w.genes,L?"":X)},update_matrix_col:async X=>{if(w.genes.svg_bar_gene.selectAll("g").attr("font-weight","normal").attr("opacity",1),w.cats.svg_bar_cluster.selectAll("g").attr("font-weight","normal").attr("opacity",w.cats.reset_cat?1:.25),w.cats.reset_cat)w.containers.bar_cluster.scrollTo({top:0,behavior:"smooth"});else{let wA=w.cats.svg_bar_cluster.selectAll("g").filter(function(){return qA(this).select("text").text()===X}).attr("opacity",1);if(!wA.empty()){let yA=wA.node().getBoundingClientRect().top,RA=w.containers.bar_cluster.getBoundingClientRect().top,UA=yA-RA+w.containers.bar_cluster.scrollTop;w.containers.bar_cluster.scrollTo({top:UA,behavior:"smooth"})}}ug(w.cats,"cluster"),Vg(w.cats,[X]),HI(w.genes,[]),iB(W,w,!w.cats.selected_cats.length>0);let L=w.cats.selected_cats.join("-");fI(W,L),$I(W,L),GB(w.genes,W);let aA=Qg(W,w.close_up);y.setProps({layers:aA}),w.genes.gene_search_input.value="",RQ(w.genes,"")},update_matrix_dendro_col:async X=>{let L=X;ug(w.cats,"cluster"),Vg(w.cats,L),HI(w.genes,[]),iB(W,w,!w.cats.selected_cats.length>0);let aA=w.cats.selected_cats.join("-");fI(W,aA),$I(W,aA),GB(w.genes,W);let wA=Qg(W,w.close_up);y.setProps({layers:wA}),w.cats.svg_bar_cluster.selectAll("g").attr("font-weight","normal").attr("opacity",w.cats.reset_cat?1:.25);let yA=L;if(!w.cats.reset_cat){let RA=w.cats.svg_bar_cluster.selectAll("g").filter(function(){return qA(this).select("text").text()===yA}).attr("opacity",1);if(!RA.empty()){let UA=RA.node().getBoundingClientRect().top,$=w.containers.bar_cluster.getBoundingClientRect().top,bg=UA-$+w.containers.bar_cluster.scrollTop;w.containers.bar_cluster.scrollTo({top:bg,behavior:"smooth"})}}},update_view_state:async(X,L,aA)=>{w.close_up=L,Ol(X,y,W,w);let wA=Qg(W,w.close_up);y.setProps({controller:{doubleClickZoom:!1},initialViewState:X,views:w.views,layers:wA})},update_layers:()=>{console.log("update_layers")},finalize:()=>{y.finalize()}}};var dV=(g,A)=>{g.tile_scatter_data=A};var UV=(g,A)=>{g.tile_names_array=A},SV=g=>{g.tile_name_to_index_map=new Map,g.tile_names_array.forEach((A,I)=>{g.tile_name_to_index_map.set(A,I)})};var LV=async g=>{let A={},I=g+"/df_colors.parquet";var B=await FQ(I,_g.fetch);let Q=[],C=[],E=B.getChild("__index_level_0__"),o=B.getChild("color");return E&&o&&(Q=E.toArray(),C=o.toArray()),Q.forEach((e,D)=>{A[String(e)]=Ke(C[D])}),A};var HV=async(g,A,I)=>{let B=I.model.get("update_trigger"),Q;B.click_type==="row-label"?(Q=B.click_value,ug(I.cats,Q),await pM(I,Q)):B.click_type==="col-label"?(ug(I.cats,"cluster"),Vg(I.cats,[B.click_value])):B.click_type==="col-dendro"?(ug(I.cats,"cluster"),Vg(I.cats,B.click_value)):ug("cluster"),jh(I,A),g.setProps({layers:[A.simple_image_layer,A.square_scatter_layer]}),Q&&Q!=="cluster"&&(I.genes.gene_search_input.value=I.genes.gene_search_input.value!==Q?Q:"",await RQ(I.genes,Q))};var fV=(g,A)=>{if(g.index===-1||!g.layer)return null;let I=A.cats.tile_cats_array[g.index];return A.tooltip_cat_cell=I,cD(".deck-tooltip").style("margin-top","75px"),{html:`<div>${I}</div?`}};var IL=async(g,A,I,B,Q,C,E,o,e=1.4,D="",r=0,n=800)=>{r===0&&(r="100%");let G=document.createElement("div");G.style.height=" 800px";let w={};LN(B),HN(w,I),w.model=g,w.img={},w.img.image_layer_colors={},w.img.image_layer_sliders={},await fN(w.img,I),await uN(w,I,"cells"),w.genes={},w.genes.color_dict_gene={},w.genes.gene_names=[],w.genes.meta_gene={},w.genes.gene_counts=[],w.genes.selected_genes=[],w.genes.trx_ini_radius=1,w.genes.trx_names_array=[],w.genes.trx_data=[],w.genes.gene_text_box="",w.genes.trx_slider=document.createElement("input"),w.genes.gene_search=document.createElement("div"),w.genes.svg_bar_gene=Ve("svg"),w.cats={},w.cats.cat="cluster",w.cats.reset_cat=!1,w.cats.selected_cats=[],w.cats.cell_cats=[],w.cats.dict_cell_cats={},w.cats.color_dict_cluster={},w.cats.cluster_counts=[],w.cats.polygon_cell_names=[],w.cats.svg_bar_cluster=Ve("svg"),w.tooltip_cat_tile="",w.cats.square_tile_size=e,await Vl(w.genes,I);let k={name:"cells",color:[0,0,255]},F=I+"/tile_geometries.parquet";var h=await FQ(F,_g.fetch);w.cats.tile_cats_array=h.getChild("cluster").toArray(),w.cats.tile_exp_array=[],w.cats.tile_names_array=[],w.cats.tile_scatter_data=[],dV(w.cats,Jn(h)),UV(w.cats,h.getChild("name").toArray()),SV(w.cats),w.cats.tile_color_dict=await LV(I);let y=await c8(w,k),J=h8(w.cats),M={simple_image_layer:y,square_scatter_layer:J};w.views=Pl();let l=w8(G,r,n),Y={target:[Q,C,E],zoom:o};l.setProps({views:w.views,layers:[M.simple_image_layer,M.square_scatter_layer],getTooltip:x=>fV(x,w),initialViewState:Y}),Object.keys(w.model).length>0&&w.model.on("change:update_trigger",()=>HV(l,M,w)),y8(l,M,w);let U=eV(l,M,w);return A.appendChild(U),A.appendChild(G),()=>l.finalize()};var SnA=({isDragging:g})=>g?"grabbing":"pointer",uV=(g,A,I)=>(typeof A=="number"&&(A=A+100,I=I+100),new ca({parent:g,getCursor:SnA,width:A,height:I}));var mV=(g,A)=>{let I;g.mat.forEach((B,Q)=>{B.forEach((C,E)=>{C>=0?I=[255,0,0]:I=[0,0,255];let o={position:[A.viz.col_offset*(E+.5),A.viz.row_offset*(Q+1.5)],color:[I[0],I[1],I[2],255*Math.abs(C)/A.mat.max_abs_value],value:C,row:Q,col:E};A.mat.mat_data.push(o)})})};var xV=(g,A,I,B,Q,C,E,o)=>{let e={};return e.root=I,e.model=g,e.custom_callbacks={},e.custom_callbacks.row=C,e.custom_callbacks.col=E,e.custom_callbacks.col_dendro=o,e.viz={},e.viz.height_margin=100,e.cats={},e.cats.num_cats={},e.cats.num_cats.row=0,e.cats.num_cats.col=0,e.root.style.height=Q+e.viz.height_margin+"px",e.viz.mat_width=B,e.viz.mat_height=Q,e.mat={},e.mat.num_rows=A.mat.length,e.mat.num_cols=A.mat[0].length,e.row_nodes=A.row_nodes,e.col_nodes=A.col_nodes,e.mat.net_mat=A.mat,e.linkage=A.linkage,e.viz.base_font_size=125,e.viz.col_label=75,e.viz.row_label=75,e.viz.extra_space={},e.viz.extra_space.row=10,e.viz.extra_space.col=10,e.zoom={},e.zoom.ini_zoom_x=0,e.zoom.ini_zoom_y=0,e.viz.row_cat_width=9,e.viz.col_cat_height=9,e.viz.row_cat_offset=10,e.viz.col_cat_offset=10,e.viz.label_row_x=15,e.viz.label_col_y=25,e.viz.cat_shift_row=30,e.viz.label_buffer=1,e.animate={},e.animate.duration=2500,e.viz.dendrogram_width=15,e.viz.font_size={},e.viz.font_size.rows=e.viz.base_font_size/e.mat.num_rows,e.viz.font_size.cols=e.viz.base_font_size/e.mat.num_cols,e.viz.col_region=(e.viz.col_cat_height+e.viz.extra_space.col)*e.cats.num_cats.col+e.viz.col_label,e.viz.row_region=(e.viz.row_cat_width+e.viz.extra_space.row)*e.cats.num_cats.row+e.viz.row_label,e.viz.col_width=e.viz.mat_width/e.mat.num_cols,e.viz.row_offset=e.viz.mat_height/e.mat.num_rows,e.viz.col_offset=e.viz.mat_width/e.mat.num_cols,e.viz.cat_shift_col=e.viz.col_label,e.zoom.ini_pan_x=e.viz.mat_width/2,e.zoom.ini_pan_y=e.viz.mat_height/2+e.viz.row_offset,e.mat.mat_data=[],e.mat.num_rows=A.mat.length,e.mat.num_cols=A.mat[0].length,e.mat.max_abs_value=A.mat.flat().reduce((D,r)=>Math.max(D,Math.abs(r)),-1/0),e.order={},e.order.current={},e.order.current.row="clust",e.order.current.col="clust",e.order.new="ini",e.buttons={},e.buttons.blue="#8797ff",e.buttons.gray="#EEEEEE",e.click={},e.click.type,e.click.value,e};var bV=(g,A)=>{let I=[];g.col_nodes.forEach((B,Q)=>{let C={name:B.name,ini:B.ini,clust:B.clust,rank:B.rank,rankvar:B.rankvar,index:Q};I.push(C)}),A.labels.col_label_data=I,A.labels.clicks.col=0,A.mat.orders.col={},A.mat.orders.col.ini=I.map(B=>B.ini),A.mat.orders.col.clust=I.map(B=>B.clust+1),A.mat.orders.col.rank=I.map(B=>B.rank+1),A.mat.orders.col.rankvar=I.map(B=>B.rankvar+1)},TV=(g,A)=>{let I=[];g.row_nodes.forEach((B,Q)=>{let C={name:B.name,ini:B.ini,clust:B.clust,rank:B.rank,rankvar:B.rankvar,index:Q};I.push(C)}),A.labels.row_label_data=I,A.labels.clicks.row=0,A.mat.orders.row={},A.mat.orders.row.ini=I.map(B=>B.ini),A.mat.orders.row.clust=I.map(B=>B.clust+1),A.mat.orders.row.rank=I.map(B=>B.rank+1),A.mat.orders.row.rankvar=I.map(B=>B.rankvar+1)};var WV=(g,A)=>{var I=0;let B=0;var Q=A.mat.num_rows*A.cats.num_cats.row;return new Array(Q).fill(0).map(()=>{var E=B%A.cats.num_cats.row;B%A.cats.num_cats.row===0&&(I+=1);let o={position:[A.viz.row_cat_offset*(E+.5)+20,A.viz.row_offset*(I+.5)],color:[0,255,0,255],name:"something "+I};return B+=1,o})},ZV=(g,A)=>{var I=A.mat.num_cols*A.cats.num_cats.col,B=0;let Q=0;return new Array(I).fill(0).map(()=>{var E=Q%A.mat.num_cols;Q%A.mat.num_cols===0&&(B+=1);let o={position:[A.viz.col_offset*(E+.5),A.viz.col_cat_offset*(B+1.5)-35],color:[0,255,0,150],name:"some column "+E};return Q+=1,o})};var PV=`#version 300 es
1726
1726
  #define SHADER_NAME scatterplot-layer-vertex-shader
1727
1727
 
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1728
  // customize the vertex shader to allow for x and y scaling and zooming