select_meta
selected_leidens
dendro_selected_genes
function make_dashboard(){
console.log('--- make_dashboard\n--------------------')
// Landscape or Portrait
/////////////////////////////////
// landscape should have flex and display style and have less height
if (orientation === 'landscape'){
var dashboard_html = html`
<div id='dashboard' style="height: 1050px; border:1px;">
<div style="display: flex;">
<div>
<div style="display: flex; margin-top: 20px">
<div style="margin-left: 15px; margin-right: -20px; border:1px; text-align:right;">${viewof map_type} </div>
<div id="meta_dropdown", style="margin-right: 15px; border:1px; text-align:right;">${viewof select_meta_dropdown} </div>
<div style="margin-right: 15px; border:1px; text-align:left;">${viewof cell_min_radius} </div>
</div>
<div style="margin-top: 100px; border:1px ">${container} </div>
</div>
<div style="margin-top:-10px; ">${viewof cgm}</div>
</div>
</div>
`
} else {
var dashboard_html = html`
<div id='dashboard' style="height: 2000px; border:1px;">
<div>
<div>
<div style="display: flex; margin-top: 20px">
<div style="margin-left: 15px; margin-right: -20px; border:1px; text-align:right;">${viewof map_type} </div>
<div id="meta_dropdown", style="margin-right: 15px; border:1px; text-align:right;">${viewof select_meta_dropdown} </div>
<div style="margin-right: 15px; border:1px; text-align:left;">${viewof cell_min_radius} </div>
</div>
<div style="margin-top: 100px; border:1px ">${container} </div>
</div>
<div style="margin-top:-10px; ">${viewof cgm}</div>
</div>
</div>
`
}
// <div style="margin-right: 15px; border:1px; text-align:left;">${viewof cell_opacity} </div>
return dashboard_html
}
orientation = 'portrait'
container = {
console.log('--- make container with id the-container\n---------------------')
return html `<div id='the-container' style="height:800px; width:800px; border-style:solid; border-color:#d3d3d3; border-width:1px; position: relative;"></div>`
}
check_gex_dict = gex_dict
// // cell_data = inputs['data'].map(x => {
// // x.tooltip_name = 'Leiden-' + x.leiden
// // return x
// // })
// cell_data = data.map(x => {
// x.tooltip_name = 'Leiden-' + x.leiden
// return x
// })
cat_name = 'leiden'
mutable select_cat = 'all'
check_ini_cat = ini_cat
// radius_min_pixels = 5
cell_metadata = Object.keys(data[0]).filter(x => non_param_cols.includes(x) === false)
meta_data_cols = cell_metadata.concat(all_genes)
all_genes = Object.keys(gex_dict).sort()
check_all_genes = all_genes
mutable selected_leidens = []
zoom = 1
min_zoom = zoom - 1
cell_opacity = 0.9
// viewof cell_opacity = slider({
// value: 1.00,
// min: 0.0,
// max: 1.0,
// precision: 2,
// description: "cell opacity",
// })
ini_min_radius = 1
viewof cell_min_radius = slider({
value: ini_min_radius,
min: 0.1,
max: 5.0,
precision: 2,
description: "min cell size"
})
cell_layer = new deck.ScatterplotLayer({
id: 'cell_layer',
// data: cell_data,
data: data,
getPosition: apply_map_morph,
getFillColor: d => {
var inst_color = [25, 25, 25, 255]
if (select_meta === 'none'){
// default coloring
////////////////////////////////////////
inst_color = [50, 50, 50, 100]
} else if (select_meta === 'leiden') {
// // color by category
// ////////////////////////////////////////
// if (select_cat === 'all'){
// var rgb = d3.color(cat_colors[d[select_meta]])
// inst_color = [rgb.r, rgb.g, rgb.b, 255 * cat_opacity]
// } else {
// inst_color = [50, 50, 50, 25]
// if (d[select_meta] === select_cat){
// var rgb = d3.color(cat_colors[d[select_meta]])
// inst_color = [rgb.r, rgb.g, rgb.b, 255 * cat_opacity]
// }
// }
if (selected_leidens.length === 0){
// single leiden
///////////////////
var rgb = d3.color(cat_colors[d[select_meta]])
inst_color = [rgb.r, rgb.g, rgb.b, 255 * cat_opacity]
} else {
// multiple leidens
/////////////////////
if (selected_leidens.includes(d['leiden'])){
var rgb = d3.color(cat_colors[d[select_meta]])
inst_color = [rgb.r, rgb.g, rgb.b, 255 * cat_opacity]
} else {
inst_color = [50, 50, 50, 10]
}
}
} else if (select_meta === 'mean-gene') {
// mean gene expression
////////////////////////////////////////
inst_color = [0, 0, 0, 255]
} else {
// console.log('color by single gene')
// single gene expression
////////////////////////////////////////
if (all_genes.includes(select_meta)){
// console.log('all_genes includes select_meta', select_meta)
// console.log(d.name)
// console.log(gex_dict)
// console.log(gex_dict[select_meta])
// console.log(d.name in gex_dict[select_meta])
if (d.name in gex_dict[select_meta]){
// console.log('name in gex_dict')
var inst_expression = gex_dict[select_meta][d.name]
var inst_opacity = opacity_scale(inst_expression)
inst_color = [255, 0, 0, inst_opacity]
} else {
inst_color = [50, 50, 50, 2]
}
}
// else {
// console.log('all genes does not include select_meta')
// console.log(all_genes.includes(select_meta))
// }
}
return inst_color
},
getRadius: cell_radius,
pickable: is_pickable,
highlightColor: d => [50, 50, 50],
radiusMinPixels: cell_min_radius,
opacity: cell_opacity,
updateTriggers: {
getFillColor: [select_meta, selected_leidens, gex_dict], // , mean_gene_data],
getPosition: map_type,
},
transitions: transitions,
onClick: (info, event) => {
console.log(info.object[cat_name])
if (mutable selected_leidens[0] !== info.object[cat_name]){
mutable select_meta = 'leiden'
mutable selected_leidens = [info.object[cat_name]]
d3.select('#meta_dropdown').select('select').node().value = 'none'
} else {
mutable select_meta = 'leiden'
mutable selected_leidens = []
d3.select('#meta_dropdown').select('select').node().value = 'leiden'
}
}
})
layers = [cell_layer]
deckgl.setProps({layers: layers});
flipY = false
view = new deck.OrthographicView({id: 'ortho', flipY: flipY})
deckgl = {
console.log('--- deckgl\n----------')
var deckgl = new deck.DeckGL({
container,
width: '800px',
height: '800px',
top: '175px',
views:[view],
initialViewState: initial_view_state,
// controller: true,
controller: {doubleClickZoom: false},
// getTooltip: ({object}) => {
// return object &&
// `${object['name']}`
// // `pos: ${object.x}, ${object['y']}\n`
// },
getTooltip: ({object}) => object && {
html: `${object[cat_name]}`,
style: {
fontSize: '0.8em',
padding: '5px',
}
},
// onViewStateChange: ({viewState}) => {
// debounced_something(viewState)
// return viewState
// },
// onClick: ({info}) => {
// console.log(info)
// return info
// }
});
// // shift downwards
// console.log('wait to move down move down')
// console.log('is empty', d3.select('#the-container').empty())
// d3.select('#the-container div').style('top', '150px')
// d3.select('#the-container canvas').style('top', '150px')
return deckgl
}
gex_opacity_contrast_scale = 1
opacity_scale = d3.scaleLinear()
.domain([0, meta_max * gex_opacity_contrast_scale])
.range([0, 255])
meta_max = {
var meta_max
if (select_meta in gex_dict){
meta_max = d3.max(Object.values(gex_dict[select_meta]))
} else if (select_meta === 'mean-gene') {
// set up calculation of mean gene max
meta_max = 0
} else {
meta_max = 0
}
return meta_max
}
// row_selection = Generators.observe(notify => {
// const mousemove = () => {
// // if (cgm.params.tooltip.tooltip_type.includes('dendro')){
// if (cgm.params.tooltip.tooltip_type === 'row-dendro'){
// mutable select_meta = 'mean-gene'
// mutable dendro_selected_genes = cgm.params.dendro.selected_clust_names
// }
// }
// viewof cgm.addEventListener("click", mousemove);
// // notify(cgm.params.dendro.selected_clust_names.map(x => x.replace('Leiden-', '')));
// return () => viewof cgm.removeEventListener("mousemove", mousemove);
// })
col_selection = Generators.observe(notify => {
const mousemove = () => {
if (cgm.params.tooltip.tooltip_type === 'col-dendro'){
mutable select_meta = 'leiden'
mutable dendro_selected_genes = []
mutable selected_leidens = cgm.params.dendro.selected_clust_names.map(x => x.replace('Leiden-', ''))
}
}
viewof cgm.addEventListener("click", mousemove);
notify(cgm.params.dendro.selected_clust_names.map(x => x.replace('Leiden-', '')));
return () => viewof cgm.removeEventListener("mousemove", mousemove);
})
heatmap_row = Generators.observe(notify => {
const mouse_click = () => {
// clicking gene row
//////////////////////////////
if (cgm.params.tooltip.tooltip_type === 'row-label'){
var inst_name = cgm.params.int.mouseover.row.name
mutable dendro_selected_genes = []
mutable select_meta = inst_name
d3.select('#meta_dropdown').select('select').node().value = inst_name
}
notify(cgm.params.int.mouseover.row.name)
}
viewof cgm.addEventListener("click", mouse_click);
notify(cgm.params.int.mouseover.row.name);
return () => viewof cgm.removeEventListener("mousemove", mouse_click);
})
heatmap_col = Generators.observe(notify => {
const mouse_click = () => {
// clicking cluster col
//////////////////////////////
if (cgm.params.tooltip.tooltip_type === 'col-label'){
mutable select_meta = 'leiden'
mutable dendro_selected_genes = []
mutable selected_leidens = [cgm.params.int.mouseover.col.name.replace('Leiden-', '')]
// if (mutable selected_leidens[0] !== info.object[cat_name]){
// mutable select_meta = 'leiden'
// mutable selected_leidens = [info.object[cat_name]]
// d3.select('#meta_dropdown').select('select').node().value = 'none'
// } else {
// mutable select_meta = 'leiden'
// mutable selected_leidens = []
// d3.select('#meta_dropdown').select('select').node().value = 'leiden'
// }
}
notify([cgm.params.int.mouseover.col.name])
}
viewof cgm.addEventListener("click", mouse_click);
notify([cgm.params.int.mouseover.col.name]);
return () => viewof cgm.removeEventListener("mousemove", mouse_click);
})
pako = require('pako/dist/pako.min.js')
import {slider, select} from '@jashkenas/inputs'
// mean_gene_data = Object.keys(mean_gene_data_ini).map(x => mean_gene_data_ini[x])
// gene_data_url = 'https://raw.githubusercontent.com/cornhundred/testing_something/master/per-gene-counts_slice-1_replicate-2/' + select_meta + '.csv'
// mean_opacity_scale = d3.scaleLinear()
// .domain([0, mean_gene_max])
// .range([0, 250])
// // the maximum opacity will happen when the value reaches 90% of the maximum
// gene_max = Math.max.apply(Math, gene_data.map(function(x) { return parseInt(x[select_meta]) })) * 0.90
// mean_gene_max = Math.max.apply(Math, mean_gene_data.map(function(x) { return parseInt(x['mean-gene']) })) * 0.90
// promised_selected_genes = Promise.all(dendro_selected_genes.map(gene => {
// const url = 'https://raw.githubusercontent.com/cornhundred/testing_something/master/per-gene-counts_slice-1_replicate-2_zip/' + String(gene) + '.csv.zip'
// const unzipped_csv = load_zip_csv(url)
// return unzipped_csv
// }))
// mean_gene_data_ini = {
// // selected dendro genes
// ///////////////////////////////
// var mean_gene_data_ini = {}
// promised_selected_genes.forEach((x, i) => {
// if (i === 0){
// // initialize gene_data after getting promised gene data (after dendrogram click)
// data.forEach((x,i) => {
// mean_gene_data_ini[i] = ({
// '': i,
// 'mean-gene': 0
// })
// })
// }
// const gene_name = dendro_selected_genes[i]
// // var sum_gene = d3.sum(x, d => d[gene_name])
// x.forEach((cell_obj, cell_index) => {
// mean_gene_data_ini[cell_index]['mean-gene'] = mean_gene_data_ini[cell_index]['mean-gene'] + cell_obj[gene_name] // /sum_gene
// })
// })
// return mean_gene_data_ini
// }
Purpose-built for displays of data
Observable is your go-to platform for exploring data and creating expressive data visualizations. Use reactive JavaScript notebooks for prototyping and a collaborative canvas for visual data exploration and dashboard creation.
