mirror of
https://github.com/haniffalab/scRNA-seq_analysis.git
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scRNA-seq_analysis
This commit is contained in:
veghp
commit
82cc2d191e
188 changed files with 146184 additions and 0 deletions
629
tools/gene_expression_viewer_apps/gene_expression_viewer_apps.py
Executable file
629
tools/gene_expression_viewer_apps/gene_expression_viewer_apps.py
Executable file
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@ -0,0 +1,629 @@
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#!/usr/bin/env python3
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# -*- coding: utf-8 -*-
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"""
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Created on Fri Sep 7 11:42:51 2018
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@author: doru
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"""
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import sys
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args = sys.argv
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save_to = args[1]
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expression_data_fname = args[2]
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no_of_categories = int(args[3])
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template_str = """
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<!doctype html>
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<html lang='en'>
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<head>
|
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<meta charset='utf-8'>
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<title>3D viewer</title>
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<meta name='description' content='The HTML5 Herald'>
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<meta name='author' content='Dorin-Mirel Popescu'>
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|
||||
</head>
|
||||
|
||||
<body>
|
||||
<table>
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||||
<tr>
|
||||
<td align='left'>
|
||||
<form>
|
||||
<fieldset>
|
||||
<legend><b>Visualisation options</b></legend>
|
||||
<label for = 'particleSizeBar'>Particle size: </label>
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||||
<input type='range' name = 'particleSizeBar' min = 1 max = 14 step=0.1 oninput='setParticleSize(value)' value = 2 /><br />
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||||
|
||||
<label for = 'alphaInput'>Transparency: </label>
|
||||
<input type='range' name = 'alphaInput' min = 0 max = 1000 oninput='setAlpha(value)' value = 1000 /><br />
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||||
|
||||
<label for = 'canvasSizeInput'>Canvas size: </label>
|
||||
<input type='range' name = 'canvasSizeInput' min = 200 max = 2000 oninput='setCanvasSize(value)' value = 500 /><br />
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||||
|
||||
<label for = 'bgInput'>Dark background: </label>
|
||||
<input type='radio' name = 'bgInput' oninput='setBackground(value)' value = 'dark' />
|
||||
<label for = 'bgInput'>White background: </label>
|
||||
<input type='radio' name = 'bgInput' oninput='setBackground(value)' value = 'white' checked />
|
||||
<br />
|
||||
</fieldset>
|
||||
</form>
|
||||
</td>
|
||||
<td style='vertical-align: top' rowspan='2'>
|
||||
|
||||
<form>
|
||||
<fieldset>
|
||||
<legend><b>Colour by:</b></legend>
|
||||
<table>
|
||||
<tr>
|
||||
<td>
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<label for='colourType'><input type='radio' name='colourType' onchange='setColourBy(value)' value='gene_expression' />Gene expression: </label>
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</td>
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<td>
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<label for='geneSelector'><select name='geneSelector' id='geneSelector' onchange='selectFeature()'>gene_options_here</select></label>
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</td>
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||||
</tr>
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||||
<tr>
|
||||
<td colspan = '2' align='center'>
|
||||
<canvas id='canvasColorScale' width = 200 height=40></canvas>
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||||
</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td>
|
||||
<label for='colourType'><input type='radio' name='colourType' checked onchange='setColourBy(value)' value='category' />Category:</label>
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</td>
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||||
<td>
|
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<label for='categorySelector'><select name='categorySelector' id='categorySelector' onchange = 'setCategory()'>category_options_here</select></label>
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||||
</td>
|
||||
</tr>
|
||||
</table>
|
||||
</fieldset>
|
||||
</form>
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||||
<br />
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||||
<div>
|
||||
<fieldset>
|
||||
<legend><b>Cell types:</b></legend>
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||||
<label for='toggleRadio'><input type='checkbox' name = 'toggleRadio' id='toggleRadio' onchange='toggleAllTypes()' checked />Show all:</label>
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||||
<form id = 'typesControlPanel'>
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||||
|
||||
</form>
|
||||
</fieldset>
|
||||
</div>
|
||||
</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td style='vertical-align: text-top' >
|
||||
<canvas id='canvas' width=600 height=600></canvas>
|
||||
</td>
|
||||
</tr>
|
||||
</table>
|
||||
<script id='vertex-shader' type='x-shader/x-fragment'>
|
||||
attribute vec4 a_Position;
|
||||
attribute vec3 a_Color;
|
||||
uniform float u_basePointSize;
|
||||
uniform float u_Alpha;
|
||||
uniform int u_PaintFeatureScale;
|
||||
varying vec4 v_Color;
|
||||
void main() {
|
||||
gl_Position = a_Position;
|
||||
gl_PointSize = u_basePointSize;
|
||||
if (u_PaintFeatureScale == 0){
|
||||
v_Color = vec4(a_Color, u_Alpha);
|
||||
}
|
||||
else{
|
||||
float r = 0.0;
|
||||
float g = 0.0;
|
||||
float b = 0.0;
|
||||
r = max(0.0, 2.0 * a_Color.r - 1.0);
|
||||
b = max(0.0, 2.0 * (1.0 - a_Color.r) - 1.0);
|
||||
g = 1.0 - 2.0 * abs(a_Color.r - 0.5);
|
||||
v_Color = vec4(r, g, b, u_Alpha);
|
||||
}
|
||||
}
|
||||
</script>
|
||||
<script id ='fragment-shader' type='x-shader/x-fragment'>
|
||||
precision mediump float;
|
||||
varying vec4 v_Color;
|
||||
void main() {
|
||||
float r = 0.0;
|
||||
vec2 cxy = 2.0 * gl_PointCoord - 1.0;
|
||||
r = dot(cxy, cxy);
|
||||
if (r > 1.0){
|
||||
discard;
|
||||
}
|
||||
gl_FragColor = v_Color;
|
||||
}
|
||||
</script>
|
||||
<script type = 'text/javascript'>
|
||||
|
||||
var Matrix4 = function(opt_src) {
|
||||
var i, s, d;
|
||||
if (opt_src && typeof opt_src === 'object' && opt_src.hasOwnProperty('elements')) {
|
||||
s = opt_src.elements;
|
||||
d = new Float32Array(16);
|
||||
for (i = 0; i < 16; ++i) {
|
||||
d[i] = s[i];
|
||||
}
|
||||
this.elements = d;
|
||||
} else {
|
||||
this.elements = new Float32Array([1,0,0,0, 0,1,0,0, 0,0,1,0, 0,0,0,1]);
|
||||
}
|
||||
};
|
||||
|
||||
Matrix4.prototype.setTranslate = function(x, y, z) {
|
||||
var e = this.elements;
|
||||
e[0] = 1; e[4] = 0; e[8] = 0; e[12] = x;
|
||||
e[1] = 0; e[5] = 1; e[9] = 0; e[13] = y;
|
||||
e[2] = 0; e[6] = 0; e[10] = 1; e[14] = z;
|
||||
e[3] = 0; e[7] = 0; e[11] = 0; e[15] = 1;
|
||||
return this;
|
||||
};
|
||||
|
||||
Matrix4.prototype.setLookAt = function(eyeX, eyeY, eyeZ, centerX, centerY, centerZ, upX, upY, upZ) {
|
||||
var e, fx, fy, fz, rlf, sx, sy, sz, rls, ux, uy, uz;
|
||||
|
||||
fx = centerX - eyeX;
|
||||
fy = centerY - eyeY;
|
||||
fz = centerZ - eyeZ;
|
||||
|
||||
// Normalize f.
|
||||
rlf = 1 / Math.sqrt(fx*fx + fy*fy + fz*fz);
|
||||
fx *= rlf;
|
||||
fy *= rlf;
|
||||
fz *= rlf;
|
||||
|
||||
// Calculate cross product of f and up.
|
||||
sx = fy * upZ - fz * upY;
|
||||
sy = fz * upX - fx * upZ;
|
||||
sz = fx * upY - fy * upX;
|
||||
|
||||
// Normalize s.
|
||||
rls = 1 / Math.sqrt(sx*sx + sy*sy + sz*sz);
|
||||
sx *= rls;
|
||||
sy *= rls;
|
||||
sz *= rls;
|
||||
|
||||
// Calculate cross product of s and f.
|
||||
ux = sy * fz - sz * fy;
|
||||
uy = sz * fx - sx * fz;
|
||||
uz = sx * fy - sy * fx;
|
||||
|
||||
// Set to this.
|
||||
e = this.elements;
|
||||
e[0] = sx;
|
||||
e[1] = ux;
|
||||
e[2] = -fx;
|
||||
e[3] = 0;
|
||||
|
||||
e[4] = sy;
|
||||
e[5] = uy;
|
||||
e[6] = -fy;
|
||||
e[7] = 0;
|
||||
|
||||
e[8] = sz;
|
||||
e[9] = uz;
|
||||
e[10] = -fz;
|
||||
e[11] = 0;
|
||||
|
||||
e[12] = 0;
|
||||
e[13] = 0;
|
||||
e[14] = 0;
|
||||
e[15] = 1;
|
||||
|
||||
// Translate.
|
||||
return this.translate(-eyeX, -eyeY, -eyeZ);
|
||||
};
|
||||
|
||||
Matrix4.prototype.translate = function(x, y, z) {
|
||||
var e = this.elements;
|
||||
e[12] += e[0] * x + e[4] * y + e[8] * z;
|
||||
e[13] += e[1] * x + e[5] * y + e[9] * z;
|
||||
e[14] += e[2] * x + e[6] * y + e[10] * z;
|
||||
e[15] += e[3] * x + e[7] * y + e[11] * z;
|
||||
return this;
|
||||
};
|
||||
|
||||
Matrix4.prototype.setPerspective = function(fovy, aspect, near, far) {
|
||||
var e, rd, s, ct;
|
||||
|
||||
if (near === far || aspect === 0) {
|
||||
throw 'null frustum';
|
||||
}
|
||||
if (near <= 0) {
|
||||
throw 'near <= 0';
|
||||
}
|
||||
if (far <= 0) {
|
||||
throw 'far <= 0';
|
||||
}
|
||||
|
||||
fovy = Math.PI * fovy / 180 / 2;
|
||||
s = Math.sin(fovy);
|
||||
if (s === 0) {
|
||||
throw 'null frustum';
|
||||
}
|
||||
|
||||
rd = 1 / (far - near);
|
||||
ct = Math.cos(fovy) / s;
|
||||
|
||||
e = this.elements;
|
||||
|
||||
e[0] = ct / aspect;
|
||||
e[1] = 0;
|
||||
e[2] = 0;
|
||||
e[3] = 0;
|
||||
|
||||
e[4] = 0;
|
||||
e[5] = ct;
|
||||
e[6] = 0;
|
||||
e[7] = 0;
|
||||
|
||||
e[8] = 0;
|
||||
e[9] = 0;
|
||||
e[10] = -(far + near) * rd;
|
||||
e[11] = -1;
|
||||
|
||||
e[12] = 0;
|
||||
e[13] = 0;
|
||||
e[14] = -2 * near * far * rd;
|
||||
e[15] = 0;
|
||||
|
||||
return this;
|
||||
};
|
||||
</script>
|
||||
<script type='text/javascript'>
|
||||
|
||||
function buildCategoryRadioButtons(){
|
||||
category_type = categorySelector.options[categorySelector.selectedIndex].value;
|
||||
current_indices = indices_all;
|
||||
// create radio commands from categories
|
||||
typesControlPanel.innerHTML = "";
|
||||
radio_commands_HTML = "";
|
||||
for(name in categories_indices[category_type]){
|
||||
f_index = categories_indices[category_type][name][0]
|
||||
cols = categories_colours[category_type].slice(3 * f_index, 3 * f_index + 3)
|
||||
col_label = "#";
|
||||
for(k=0;k<cols.length;k++){col_hex = Math.round(255 * cols[k]).toString(16).padStart(2, '0'); col_label = col_label + col_hex}
|
||||
radio_command = "<div style='background-color:" + col_label + "'>";
|
||||
radio_command = radio_command + "<input style='float:left' type='checkbox' id='" + name;
|
||||
radio_command = radio_command + "' checked onchange='toggleCategoryAction()' /><label style='float:left' for='" + name + "'";
|
||||
radio_command = radio_command + ">" + name + ": </label><br/></div>"
|
||||
radio_commands_HTML = radio_commands_HTML + radio_command
|
||||
}
|
||||
typesControlPanel.innerHTML = radio_commands_HTML;
|
||||
}
|
||||
|
||||
function toggleCategoryAction(){
|
||||
updateBuffer()
|
||||
draw()
|
||||
}
|
||||
|
||||
function setCategory(){
|
||||
buildCategoryRadioButtons()
|
||||
updateBuffer()
|
||||
draw()
|
||||
}
|
||||
|
||||
function setColourBy(value){
|
||||
colour_by = value;
|
||||
if (colour_by =='category'){
|
||||
PaintFeatureScale = 0;
|
||||
}else{
|
||||
PaintFeatureScale = 1;
|
||||
}
|
||||
gl_context.uniform1i(u_PaintFeatureScale, PaintFeatureScale)
|
||||
updateBuffer()
|
||||
draw()
|
||||
}
|
||||
|
||||
|
||||
function toggleAllTypes(){
|
||||
controlRadios = typesControlPanel.elements
|
||||
for(i=0;i<controlRadios.length;i++){
|
||||
controlRadios[i].checked = toggleRadio.checked
|
||||
}
|
||||
updateBuffer()
|
||||
draw()
|
||||
}
|
||||
|
||||
function selectFeature(){
|
||||
feature = geneSelector.value
|
||||
updateBuffer()
|
||||
draw()
|
||||
console.log('selected features')
|
||||
}
|
||||
|
||||
function draw(){
|
||||
if(bg_color == "white"){
|
||||
gl_context.clearColor(1, 1, 1, 1)
|
||||
}else{
|
||||
gl_context.clearColor(0, 0, 0, 1)
|
||||
}
|
||||
gl_context.clear(gl_context.COLOR_BUFFER_BIT);
|
||||
gl_context.bufferData(gl_context.ARRAY_BUFFER, buffer_data_array, gl_context.STATIC_DRAW)
|
||||
gl_context.drawArrays(gl_context.POINTS, 0, n)
|
||||
}
|
||||
|
||||
function updateBuffer(){
|
||||
var buffer_data = [];
|
||||
// first update indices to be used - for this read the category control panel radio buttons
|
||||
controlRadios = typesControlPanel.elements
|
||||
current_indices = []
|
||||
for(i=0;i<controlRadios.length;i++){
|
||||
if(controlRadios[i].checked){
|
||||
radio_type = controlRadios[i].id
|
||||
current_indices = current_indices.concat(categories_indices[category_type][radio_type])
|
||||
}
|
||||
}
|
||||
// now just populate the buffer_data
|
||||
if(colour_by == 'gene_expression'){
|
||||
current_indices.forEach(function(index, i){
|
||||
buffer_data.push(coordinates_data[2 * index])
|
||||
buffer_data.push(coordinates_data[2 * index + 1])
|
||||
buffer_data.push(gene_expression[feature][index])
|
||||
buffer_data.push(gene_expression[feature][index])
|
||||
buffer_data.push(gene_expression[feature][index])
|
||||
})
|
||||
}else{
|
||||
current_indices.forEach(function(index, i){
|
||||
buffer_data.push(coordinates_data[2 * index])
|
||||
buffer_data.push(coordinates_data[2 * index + 1])
|
||||
buffer_data.push(categories_colours[category_type][3 * index])
|
||||
buffer_data.push(categories_colours[category_type][3 * index + 1])
|
||||
buffer_data.push(categories_colours[category_type][3 * index + 2])
|
||||
})
|
||||
}
|
||||
buffer_data_array = new Float32Array(buffer_data)
|
||||
n = buffer_data_array.length / 5
|
||||
}
|
||||
|
||||
function setParticleSize(value){
|
||||
particleSize = parseInt(value)
|
||||
gl_context.uniform1f(u_basePointSize, particleSize)
|
||||
updateBuffer()
|
||||
draw()
|
||||
}
|
||||
|
||||
function setAlpha(value){
|
||||
alphaValue = parseInt(value) / 1000
|
||||
gl_context.uniform1f(u_Alpha, alphaValue)
|
||||
updateBuffer()
|
||||
draw()
|
||||
}
|
||||
|
||||
function setCanvasSize(value){
|
||||
value = parseInt(value)
|
||||
canvas.width = value
|
||||
canvas.height = value
|
||||
gl_context = getContext(canvas)
|
||||
gl_context = initContext(gl_context)
|
||||
gl_context.viewport(0, 0, canvas.width, canvas.height)
|
||||
updateBuffer()
|
||||
draw()
|
||||
}
|
||||
|
||||
function setBackground(value){
|
||||
bg_color = value;
|
||||
draw()
|
||||
}
|
||||
|
||||
function shadersFromScriptElement(gl, ID, type){
|
||||
shaderScript = document.getElementById(ID)
|
||||
var str = ''
|
||||
var k = shaderScript.firstChild;
|
||||
while(k){
|
||||
if (k.nodeType == 3){
|
||||
str += k.textContent;
|
||||
}
|
||||
k = k.nextSibling
|
||||
}
|
||||
var shader = gl.createShader(type)
|
||||
gl.shaderSource(shader, str)
|
||||
gl.compileShader(shader)
|
||||
return shader
|
||||
}
|
||||
|
||||
function getContext(canvasWidget){
|
||||
var names = ['webgl', 'experimental-webgl', 'webkit-3d', 'moz-webgl'];
|
||||
for(var i=0; i<names.length; i++){
|
||||
try{
|
||||
var gl = canvasWidget.getContext(names[i])
|
||||
}catch(e){}
|
||||
if(gl){i=names.length}
|
||||
}
|
||||
|
||||
var vshader = shadersFromScriptElement(gl, 'vertex-shader', gl.VERTEX_SHADER),
|
||||
fshader = shadersFromScriptElement(gl, 'fragment-shader', gl.FRAGMENT_SHADER)
|
||||
program = gl.createProgram();
|
||||
gl.attachShader(program, vshader)
|
||||
gl.attachShader(program, fshader)
|
||||
gl.linkProgram(program)
|
||||
gl.useProgram(program)
|
||||
gl.program = program
|
||||
return gl
|
||||
}
|
||||
|
||||
function initContext(gl){
|
||||
n = buffer_data_array.length / 5
|
||||
var vertexColourBuffer = gl.createBuffer()
|
||||
gl.bindBuffer(gl.ARRAY_BUFFER, vertexColourBuffer)
|
||||
|
||||
var FSIZE = buffer_data_array.BYTES_PER_ELEMENT;
|
||||
|
||||
var a_Position = gl.getAttribLocation(gl.program, 'a_Position')
|
||||
gl.vertexAttribPointer(a_Position, 2, gl.FLOAT, false, FSIZE * 5, 0)
|
||||
gl.enableVertexAttribArray(a_Position)
|
||||
|
||||
var a_Color = gl.getAttribLocation(gl.program, 'a_Color')
|
||||
gl.vertexAttribPointer(a_Color, 3, gl.FLOAT, false, FSIZE * 5, 2 * FSIZE)
|
||||
gl.enableVertexAttribArray(a_Color)
|
||||
|
||||
u_basePointSize = gl.getUniformLocation(gl.program, 'u_basePointSize')
|
||||
gl.uniform1f(u_basePointSize, particleSize)
|
||||
|
||||
u_Alpha = gl.getUniformLocation(gl.program, "u_Alpha")
|
||||
gl.uniform1f(u_Alpha, alphaValue)
|
||||
|
||||
u_PaintFeatureScale = gl.getUniformLocation(gl.program, 'u_PaintFeatureScale')
|
||||
gl.uniform1i(u_PaintFeatureScale, PaintFeatureScale)
|
||||
|
||||
gl.clearColor(1, 1, 1, 1);
|
||||
if(bg_color == "dark"){
|
||||
gl.clearColor(0, 0, 0, 1)
|
||||
}
|
||||
|
||||
gl.disable(gl.DEPTH_TEST)
|
||||
gl.enable(gl.BLEND)
|
||||
gl.blendFunc(gl.SRC_ALPHA, gl.ONE_MINUS_SRC_ALPHA)
|
||||
|
||||
gl.clear(gl.COLOR_BUFFER_BIT);
|
||||
return gl
|
||||
}
|
||||
|
||||
var categorySelector = document.getElementById('categorySelector'),
|
||||
geneSelector = document.getElementById('geneSelector'),
|
||||
typesControlPanel = document.getElementById('typesControlPanel'),
|
||||
toggleRadio = document.getElementById('toggleRadio')
|
||||
|
||||
var canvas = document.getElementById('canvas'),
|
||||
particleSize = 5,
|
||||
alphaValue = 1.0,
|
||||
bg_color = "white",
|
||||
n = 0,
|
||||
particleSize = 2,
|
||||
PaintFeatureScale = 0;
|
||||
|
||||
coordinates_data = [coordinates_data_here]
|
||||
gene_expression = []; gene_expression_colour_coded;
|
||||
|
||||
categories_colours = []
|
||||
categories_colours_data_here
|
||||
categories_indices = []
|
||||
categories_indices_data_here
|
||||
|
||||
// initialize flags
|
||||
// when toggling between gene expression and category, do not slice data i.e. do not recompute index data
|
||||
// when choosing a category always re-initiate index data
|
||||
|
||||
var colour_by = 'category', // the other options is can be 'category'
|
||||
category_types = [],
|
||||
category_type = '',
|
||||
features = [],
|
||||
feature = '';
|
||||
|
||||
// set category
|
||||
for(name in categories_colours){category_types.push(name)}
|
||||
category_type = category_types[0]
|
||||
|
||||
// set feature
|
||||
for(name in gene_expression){features.push(name)}
|
||||
feature = features[0];
|
||||
|
||||
// create global data holders
|
||||
var indices_all = [],
|
||||
current_indices = [],
|
||||
current_colours = [],
|
||||
buffer_data_array = [];
|
||||
|
||||
for(j=0;j<categories_colours[category_type].length/3;j++){indices_all.push(j)}
|
||||
|
||||
// build the categories buttons for the first time
|
||||
buildCategoryRadioButtons()
|
||||
|
||||
updateBuffer()
|
||||
|
||||
// create the renderer
|
||||
var gl_context = getContext(canvas);
|
||||
gl_context = initContext(gl_context)
|
||||
|
||||
// now draw
|
||||
draw()
|
||||
|
||||
// draw the scale
|
||||
var canvasColorScale = document.getElementById('canvasColorScale'),
|
||||
canvas_ctx = canvasColorScale.getContext('2d'),
|
||||
scale_gradient = canvas_ctx.createLinearGradient(0, 0, 200, 0);
|
||||
|
||||
scale_gradient.addColorStop(0, 'blue');
|
||||
scale_gradient.addColorStop(0.5, 'green');
|
||||
scale_gradient.addColorStop(1, 'red');
|
||||
canvas_ctx.fillStyle = scale_gradient;
|
||||
canvas_ctx.fillRect(0, 20, canvasColorScale.width, canvasColorScale.height)
|
||||
canvas_ctx.fillStyle = 'black'
|
||||
canvas_ctx.fillText('0', 10, 10)
|
||||
canvas_ctx.fillText('8', 190, 10)
|
||||
</script>
|
||||
</body>
|
||||
</html>
|
||||
"""
|
||||
|
||||
import pandas as pd
|
||||
import numpy as np
|
||||
|
||||
data = pd.read_csv(expression_data_fname, index_col = None)
|
||||
|
||||
# convert Colours to r, g, b values, then to floats < 1.0
|
||||
def hexdec_to_1floats(hexdec):
|
||||
return np.array([int(hexdec[1:][i:(i+2)], 16) for i in (0, 2, 4)]) / 255.0
|
||||
|
||||
gene_names = [gene_name for gene_name in data.columns[(2 + 2 * no_of_categories):]]
|
||||
raw_expression = data.values[:, (2 + 2 * no_of_categories):]
|
||||
gene_options = []
|
||||
gene_expression_colour_coded = []
|
||||
max_expression = round(raw_expression.max())
|
||||
raw_expression /= max_expression
|
||||
for index, gene_name in enumerate(gene_names):
|
||||
gene_expression = raw_expression[:, index]
|
||||
gene_expression = [str(value)[:min(4, len(str(value)))] for value in gene_expression]
|
||||
gene_expression = ",".join(gene_expression)
|
||||
gene_expression_colour_coded.append("gene_expression['{gn}'] = [{ge}]".format(gn = gene_name, ge = gene_expression))
|
||||
gene_options.append("<option value='{gn}'>{gn}</option>".format(gn = gene_name))
|
||||
gene_options = "".join(gene_options)
|
||||
gene_expression_colour_coded = ";".join(gene_expression_colour_coded)
|
||||
|
||||
# make coordinates data string
|
||||
coordinates = data.values[:, 0:2].astype('float32')
|
||||
# next few steps are compressing the data into a stadard cube centered at (0,0,0) and L = 200
|
||||
Xrange = np.percentile(coordinates[:, 0], q = [1, 98]) * 1.2
|
||||
Yrange = np.percentile(coordinates[:, 1], q = [1, 98]) * 1.2
|
||||
center = np.array((np.mean(Xrange), np.mean(Yrange)))
|
||||
coordinates = coordinates - np.tile(center, (coordinates.shape[0], 1))
|
||||
ratio = max(np.abs(np.percentile(coordinates[:, 0], q = [1, 98]) * 1.2))
|
||||
ratio = max(ratio, max(np.abs(np.percentile(coordinates[:, 1], q = [1, 98]) * 1.2)))
|
||||
ratio = 1.0 / ratio
|
||||
coordinates = coordinates * ratio
|
||||
coordinates = ",".join([str(value)[:min(6, len(str(value)))] for value in coordinates.ravel()])
|
||||
|
||||
categories = [str(value).replace(".", " ") for value in data.columns[2:(2 + no_of_categories)]]
|
||||
categories_options = ["<option value='{cat}'>{cat}</option>".format(cat=cat) for cat in categories]
|
||||
categories_options = "".join(categories_options)
|
||||
|
||||
categories_colours = []
|
||||
categories_indices = []
|
||||
for cat_index in range(no_of_categories):
|
||||
category_name = data.columns[2 + cat_index]
|
||||
category_name = category_name.replace(".", " ")
|
||||
category_colours = [hexdec_to_1floats(colour) for colour in data.values[:, 2 + cat_index + no_of_categories]]
|
||||
category_colours = [",".join([str(value)[:min(4, len(str(value)))] for value in colour]) for colour in category_colours]
|
||||
category_colours = ",".join(category_colours)
|
||||
categories_colours.append("categories_colours['{cn}'] = [{cc}]".format(cn = category_name, cc = category_colours))
|
||||
types = [value for value in np.unique(data.values[:, 2 + cat_index])]
|
||||
cat_indices = []
|
||||
categories_indices.append("categories_indices['{cn}'] = []".format(cn = category_name))
|
||||
for t_name in types:
|
||||
indices = data.values[:, 2 + cat_index] == t_name
|
||||
indices = np.where(indices)[0]
|
||||
indices = ",".join([str(value) for value in indices])
|
||||
cat_indices.append("categories_indices['{cn}']['{tn}'] = [{ind}]".format(cn = category_name, tn = t_name, ind = indices))
|
||||
cat_indices = "\n".join(cat_indices)
|
||||
categories_indices.append(cat_indices)
|
||||
categories_indices = "\n".join(categories_indices)
|
||||
categories_colours = "\n".join(categories_colours)
|
||||
|
||||
template_str = template_str.replace('gene_options_here', gene_options)
|
||||
template_str = template_str.replace('gene_expression_colour_coded', gene_expression_colour_coded)
|
||||
template_str = template_str.replace('coordinates_data_here', coordinates)
|
||||
template_str = template_str.replace('category_options_here', categories_options)
|
||||
template_str = template_str.replace('categories_colours_data_here', categories_colours)
|
||||
template_str = template_str.replace('categories_indices_data_here', categories_indices)
|
||||
with open(save_to, 'w') as result:
|
||||
result.write(template_str)
|
||||
Loading…
Add table
Add a link
Reference in a new issue