DEGA-137-Custom-segment-arg-for-Landscape-view

js/deck-gl/cell_layer.js

@@ -90,7 +90,13 @@ const cell_layer_onclick = async (info, d, deck_ist, layers_obj, viz_state) => {
 
 export const ini_cell_layer = async (base_url, viz_state) => {
 
-    const cell_url = base_url + `/cell_metadata.parquet`;
+    let cell_url
+    if (viz_state.seg.version === 'default'){
+        cell_url = base_url + `/cell_metadata.parquet`;
+    } else {
+        cell_url = base_url + '/cell_metadata_' + viz_state.seg.version + '.parquet';
+    }
+
     var cell_arrow_table = await get_arrow_table(cell_url, options.fetch)
 
     set_cell_names_array(viz_state.cats, cell_arrow_table)
@@ -105,7 +111,9 @@ export const ini_cell_layer = async (base_url, viz_state) => {
         viz_state.cats.cell_cats = viz_state.cats.cell_names_array.map(name => viz_state.cats.meta_cell[name])
     } else {
         // default clustering
-        var cluster_arrow_table = await get_arrow_table(base_url + `/cell_clusters/cluster.parquet`, options.fetch)
+
+        var cluster_arrow_table = await get_arrow_table(base_url + `/cell_clusters${viz_state.seg.version && viz_state.seg.version !== 'default' ? '_' + viz_state.seg.version : ''}/cluster.parquet`,
+                                                        options.fetch)
         set_cell_cats(viz_state.cats, cluster_arrow_table, 'cluster')
     }
 
@@ -114,8 +122,13 @@ export const ini_cell_layer = async (base_url, viz_state) => {
     // Combine names and positions into a single array of objects
     const new_cell_names_array = cell_arrow_table.getChild("name").toArray()
 
+    console.log(cell_arrow_table)
+
     const flatCoordinateArray = viz_state.spatial.cell_scatter_data.attributes.getPosition.value;
 
+    console.log('*********************')
+    console.log(new_cell_names_array)
+
     // save cell positions and categories in one place for updating cluster bar plot
     viz_state.combo_data.cell = new_cell_names_array.map((name, index) => ({
         name: name,

js/deck-gl/trx_layer.js

@@ -30,7 +30,7 @@ const trx_layer_callback = async (info, d, deck_ist, layers_obj, viz_state) => {
     update_selected_genes(viz_state.genes, [inst_gene])
     update_selected_cats(viz_state.cats, [])
 
-    await update_cell_exp_array(viz_state.cats, viz_state.genes, viz_state.global_base_url, inst_gene)
+    await update_cell_exp_array(viz_state.cats, viz_state.genes, viz_state.global_base_url, inst_gene, viz_state.seg.version)
 
     update_cell_layer_id(layers_obj, new_cat)
 

js/global_variables/cell_exp_array.js

@@ -1,16 +1,33 @@
 import { get_arrow_table } from '../read_parquet/get_arrow_table'
 import { options } from '../global_variables/fetch_options.js'
 
-export const update_cell_exp_array = async (cats, genes, base_url, inst_gene) => {
+export const update_cell_exp_array = async (cats, genes, base_url, inst_gene, version) => {
 
-    var file_path = base_url + '/cbg/' + inst_gene + '.parquet'
+    let file_path;
+    if (version === 'default'){
+        file_path = base_url + '/cbg/' + inst_gene + '.parquet';
+    } else {
+        file_path = base_url + '/cbg_' + version + '/' + inst_gene + '.parquet';
+    }
+
+    //var file_path = base_url + '/cbg/' + inst_gene + '.parquet'
     var exp_table = await get_arrow_table(file_path, options.fetch)
     let cell_names = exp_table.getChild('__index_level_0__').toArray()
     let cell_exp = exp_table.getChild(inst_gene).toArray()
 
     const new_exp_array = new Array(cats.cell_names_array.length).fill(0)
 
+    Object.entries(cats.cell_name_to_index_map).forEach(([key, value]) => {
+        console.log(`${key}: ${value}`);
+    });
+
+    console.log(cats.cell_names_array.length)
+    console.log(cats.cell_name_to_index_map.get('127062'))
+
     cell_names.forEach((name, i) => {
+        name = String(name)
+        //console.log(name, typeof name)
+
         if (cats.cell_name_to_index_map.has(name)) {
             const index = cats.cell_name_to_index_map.get(name);
             const exp_value = Number(cell_exp[i]);

js/global_variables/cell_names_array.js

@@ -4,6 +4,8 @@ export const set_cell_names_array = (cats, cell_arrow_table) => {
 
 export const set_cell_name_to_index_map = (cats) => {
     cats.cell_names_array.forEach((name, index) => {
+        console.log(name, typeof name)
+        name = String(name)
         cats.cell_name_to_index_map.set(name, index)
     })
 }

js/ui/bar_plot.js

@@ -93,7 +93,7 @@ export const bar_callback_gene = async (event, d, deck_ist, layers_obj, viz_stat
     update_cat(viz_state.cats, new_cat)
     update_selected_genes(viz_state.genes, [inst_gene])
     update_selected_cats(viz_state.cats, [])
-    await update_cell_exp_array(viz_state.cats, viz_state.genes, viz_state.global_base_url, inst_gene)
+    await update_cell_exp_array(viz_state.cats, viz_state.genes, viz_state.global_base_url, inst_gene, viz_state.seg.version)
 
     update_cell_layer_id(layers_obj, new_cat)
     update_path_layer_id(layers_obj, new_cat)

js/ui/gene_search.js

@@ -56,7 +56,7 @@ const ist_gene_search_callback = async (deck_ist, layers_obj, viz_state) => {
         const inst_gene_in_gene_names = viz_state.genes.gene_names.includes(inst_gene)
 
         if (inst_gene_in_gene_names) {
-            await update_cell_exp_array(viz_state.cats, viz_state.genes, viz_state.global_base_url, inst_gene)
+            await update_cell_exp_array(viz_state.cats, viz_state.genes, viz_state.global_base_url, inst_gene, viz_state.seg.version)
         }
 
         toggle_image_layers_and_ctrls(layers_obj, viz_state, !inst_gene_in_gene_names)

js/viz/landscape_ist.js

@@ -49,9 +49,13 @@ export const landscape_ist = async (
     meta_cluster={},
     umap={},
     landscape_state='spatial',
+    segmentation='default',
     view_change_custom_callback=null
 ) => {
 
+    console.log('checking segmentation', segmentation)
+
+
     if (width === 0){
         width = '100%'
     }
@@ -240,6 +244,10 @@ export const landscape_ist = async (
     viz_state.edit.visible = false
     viz_state.edit.modify_index = null
 
+    // starting to set up custom segmentation support
+    viz_state.seg = {}
+    viz_state.seg.version = segmentation
+
     if (Object.keys(viz_state.model).length !== 0){
 
         if (Object.keys(viz_state.model.get('region')).length === 0) {
@@ -365,7 +373,7 @@ export const landscape_ist = async (
             update_cat(viz_state.cats, new_cat)
             update_selected_genes(viz_state.genes, [inst_gene])
             update_selected_cats(viz_state.cats, [])
-            await update_cell_exp_array(viz_state.cats, viz_state.genes, viz_state.global_base_url, inst_gene)
+            await update_cell_exp_array(viz_state.cats, viz_state.genes, viz_state.global_base_url, inst_gene, viz_state.seg.version)
 
             update_cell_layer_id(layers_obj, new_cat)
             update_path_layer_id(layers_obj, new_cat)

js/widget.js

@@ -34,6 +34,7 @@ export const render_landscape_ist = async ({ model, el }) => {
     const meta_cluster = model.get('meta_cluster')
     const umap = model.get('umap')
     const landscape_state = model.get('landscape_state')
+    const segmentation = model.get('segmentation')
 
     return landscape_ist(
         el,
@@ -51,7 +52,8 @@ export const render_landscape_ist = async ({ model, el }) => {
         meta_cell,
         meta_cluster,
         umap,
-        landscape_state
+        landscape_state,
+        segmentation
     )
 
 }

js/widget_interactions/update_ist_landscape_from_cgm.js

@@ -38,7 +38,7 @@ export const update_ist_landscape_from_cgm = async (deck_ist, layers_obj, viz_st
             update_cat(viz_state.cats, new_cat)
             update_selected_genes(viz_state.genes, [inst_gene])
             update_selected_cats(viz_state.cats, [])
-            await update_cell_exp_array(viz_state.cats, viz_state.genes, viz_state.global_base_url, inst_gene)
+            await update_cell_exp_array(viz_state.cats, viz_state.genes, viz_state.global_base_url, inst_gene, viz_state.seg.version)
 
             update_cell_layer_id(layers_obj, new_cat)
             update_path_layer_id(layers_obj, new_cat)