| Next changeset 1:4bf852448b5d (2024-02-28) |
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Commit message:
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1 |
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added:
gate_finder.py index.html main_macros.xml static/css/2.f290e260.chunk.css static/css/2.f290e260.chunk.css.map static/css/main.a53cc462.chunk.css static/css/main.a53cc462.chunk.css.map static/js/2.eb2fd6ea.chunk.js static/js/2.eb2fd6ea.chunk.js.LICENSE.txt static/js/2.eb2fd6ea.chunk.js.map static/js/main.303f671d.chunk.js static/js/main.303f671d.chunk.js.map static/js/runtime-main.784d90f4.js static/js/runtime-main.784d90f4.js.map static/media/complement.c220ca8c.svg static/media/intersection.b0003109.svg static/media/menu.bc56e94a.svg static/media/near_me.2a308adc.svg static/media/selection_lasso.00e80a33.svg static/media/selection_rectangle.aa477261.svg static/media/union.de5168c6.svg test-data/cropped_reactive_core.ome.tiff test-data/cropped_tutorial_data_pheno.h5ad test-data/tutorial_vitessce.html vitessce_spatial.py vitessce_spatial.xml |
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| diff -r 000000000000 -r 9f60ef2d586e gate_finder.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/gate_finder.py Thu Sep 08 17:23:33 2022 +0000 |
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| @@ -0,0 +1,156 @@ +import argparse +import json +import warnings +from pathlib import Path + +import numpy as np +import pandas as pd +from anndata import read_h5ad +from sklearn.mixture import GaussianMixture +from sklearn.preprocessing import MinMaxScaler +from vitessce import ( + AnnDataWrapper, + Component as cm, + MultiImageWrapper, + OmeTiffWrapper, + VitessceConfig, +) + + +# Generate binarized phenotype for a gate +def get_gate_phenotype(g, d): + dd = d.copy() + dd = np.where(dd < g, 0, dd) + np.warnings.filterwarnings('ignore') + dd = np.where(dd >= g, 1, dd) + return dd + + +def get_gmm_phenotype(data): + low = np.percentile(data, 0.01) + high = np.percentile(data, 99.99) + data = np.clip(data, low, high) + + sum = np.sum(data) + median = np.median(data) + data_med = data / sum * median + + data_log = np.log1p(data_med) + data_log = data_log.reshape(-1, 1) + + scaler = MinMaxScaler(feature_range=(0, 1)) + data_norm = scaler.fit_transform(data_log) + + gmm = GaussianMixture(n_components=2) + gmm.fit(data_norm) + gate = np.mean(gmm.means_) + + return get_gate_phenotype(gate, np.ravel(data_norm)) + + +def main(inputs, output, image, anndata, masks=None): + """ + Parameter + --------- + inputs : str + File path to galaxy tool parameter. + output : str + Output folder for saving web content. + image : str + File path to the OME Tiff image. + anndata : str + File path to anndata containing phenotyping info. + masks : str + File path to the image masks. + """ + warnings.simplefilter('ignore') + + with open(inputs, 'r') as param_handler: + params = json.load(param_handler) + + marker = params['marker'].strip() + from_gate = params['from_gate'] + to_gate = params['to_gate'] + increment = params['increment'] + x_coordinate = params['x_coordinate'].strip() or 'X_centroid' + y_coordinate = params['y_coordinate'].strip() or 'Y_centroid' + + adata = read_h5ad(anndata) + + # If no raw data is available make a copy + if adata.raw is None: + adata.raw = adata + + # Copy of the raw data if it exisits + if adata.raw is not None: + adata.X = adata.raw.X + + data = pd.DataFrame( + adata.X, + columns=adata.var.index, + index=adata.obs.index + ) + marker_values = data[[marker]].values + marker_values_log = np.log1p(marker_values) + + # Identify the list of increments + gate_names = [] + for num in np.arange(from_gate, to_gate, increment): + num = round(num, 3) + key = marker + '--' + str(num) + adata.obs[key] = get_gate_phenotype(num, marker_values_log) + gate_names.append(key) + + adata.obs['GMM_auto'] = get_gmm_phenotype(marker_values) + gate_names.append('GMM_auto') + + adata.obsm['XY_coordinate'] = adata.obs[[x_coordinate, y_coordinate]].values + + vc = VitessceConfig(name=None, description=None) + dataset = vc.add_dataset() + image_wrappers = [OmeTiffWrapper(img_path=image, name='OMETIFF')] + if masks: + image_wrappers.append( + OmeTiffWrapper(img_path=masks, name='MASKS', is_bitmask=True) + ) + dataset.add_object(MultiImageWrapper(image_wrappers)) + + dataset.add_object( + AnnDataWrapper( + adata, + spatial_centroid_obsm='XY_coordinate', + cell_set_obs=gate_names, + cell_set_obs_names=[obj[0].upper() + obj[1:] for obj in gate_names], + expression_matrix="X" + ) + ) + spatial = vc.add_view(dataset, cm.SPATIAL) + cellsets = vc.add_view(dataset, cm.CELL_SETS) + status = vc.add_view(dataset, cm.STATUS) + lc = vc.add_view(dataset, cm.LAYER_CONTROLLER) + genes = vc.add_view(dataset, cm.GENES) + cell_set_sizes = vc.add_view(dataset, cm.CELL_SET_SIZES) + cell_set_expression = vc.add_view(dataset, cm.CELL_SET_EXPRESSION) + + vc.layout( + (status / genes / cell_set_expression) + | (cellsets / cell_set_sizes / lc) + | (spatial) + ) + config_dict = vc.export(to='files', base_url='http://localhost', out_dir=output) + + with open(Path(output).joinpath('config.json'), 'w') as f: + json.dump(config_dict, f, indent=4) + + +if __name__ == '__main__': + aparser = argparse.ArgumentParser() + aparser.add_argument("-i", "--inputs", dest="inputs", required=True) + aparser.add_argument("-e", "--output", dest="output", required=True) + aparser.add_argument("-g", "--image", dest="image", required=True) + aparser.add_argument("-a", "--anndata", dest="anndata", required=True) + aparser.add_argument("-m", "--masks", dest="masks", required=False) + + args = aparser.parse_args() + + main(args.inputs, args.output, args.image, args.anndata, args.masks) |
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| diff -r 000000000000 -r 9f60ef2d586e index.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/index.html Thu Sep 08 17:23:33 2022 +0000 |
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| @@ -0,0 +1,39 @@ +<!doctype html> +<html lang="en"> + <head> + <meta charset="utf-8"> + <style> + body,html{height:100%} + body{ + font-family:-apple-system,'Helvetica Neue',Arial,sans-serif;display:flex;flex-direction:column} + #full-app{flex:1} + #full-app .vitessce-container{ + height:max(100%,100vh);width:100%;overflow:hidden} + #full-app #small-app .vitessce-container{height:600px} + </style> + <title>Vitessce</title> + <link href="./static/css/2.f290e260.chunk.css" rel="stylesheet"> + <link href="./static/css/main.a53cc462.chunk.css" rel="stylesheet"> + </head> + <body> + <div id="full-app"> + <div class="container-fluid"> + <div class="row p-2"> + <div class="col col-full"> + <h1>Vitessce is loading...</h1> + <div style="width:1000px"> + <div id="small-app"> + </div> + </div> + </div> + </div> + </div> + </div> + <noscript>You need to enable JavaScript to run this app.</noscript> + <script> + !function(e){function t(t){for(var n,i,l=t[0],f=t[1],a=t[2],p=0,s=[];p<l.length;p++)i=l[p],Object.prototype.hasOwnProperty.call(o,i)&&o[i]&&s.push(o[i][0]),o[i]=0;for(n in f)Object.prototype.hasOwnProperty.call(f,n)&&(e[n]=f[n]);for(c&&c(t);s.length;)s.shift()();return u.push.apply(u,a||[]),r()}function r(){for(var e,t=0;t<u.length;t++){for(var r=u[t],n=!0,l=1;l<r.length;l++){var f=r[l];0!==o[f]&&(n=!1)}n&&(u.splice(t--,1),e=i(i.s=r[0]))}return e}var n={},o={1:0},u=[];function i(t){if(n[t])return n[t].exports;var r=n[t]={i:t,l:!1,exports:{}};return e[t].call(r.exports,r,r.exports,i),r.l=!0,r.exports}i.m=e,i.c=n,i.d=function(e,t,r){i.o(e,t)||Object.defineProperty(e,t,{enumerable:!0,get:r})},i.r=function(e){"undefined"!=typeof Symbol&&Symbol.toStringTag&&Object.defineProperty(e,Symbol.toStringTag,{value:"Module"}),Object.defineProperty(e,"__esModule",{value:!0})},i.t=function(e,t){if(1&t&&(e=i(e)),8&t)return e;if(4&t&&"object"==typeof e&&e&&e.__esModule)return e;var r=Object.create(null);if(i.r(r),Object.defineProperty(r,"default",{enumerable:!0,value:e}),2&t&&"string"!=typeof e)for(var n in e)i.d(r,n,function(t){return e[t]}.bind(null,n));return r},i.n=function(e){var t=e&&e.__esModule?function(){return e.default}:function(){return e};return i.d(t,"a",t),t},i.o=function(e,t){return Object.prototype.hasOwnProperty.call(e,t)},i.p="./";var l=this.webpackJsonpvitessce=this.webpackJsonpvitessce||[],f=l.push.bind(l);l.push=t,l=l.slice();for(var a=0;a<l.length;a++)t(l[a]);var c=f;r()}([]) + </script> + <script src="./static/js/2.eb2fd6ea.chunk.js"></script> + <script src="./static/js/main.303f671d.chunk.js"></script> + </body> +</html> \ No newline at end of file |
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| diff -r 000000000000 -r 9f60ef2d586e main_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/main_macros.xml Thu Sep 08 17:23:33 2022 +0000 |
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| @@ -0,0 +1,84 @@ +<macros> + <token name="@TOOL_VERSION@">1.0.4</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@PROFILE@">20.01</token> + + <xml name="vitessce_requirements"> + <requirements> + <container type="docker">quay.io/goeckslab/vitessce:@TOOL_VERSION@</container> + </requirements> + </xml> + + <xml name="macro_stdio"> + <stdio> + <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" /> + </stdio> + </xml> + + <xml name="vitessce_cmd" token_tool_id="vitessce_spatial"> + <command> + <![CDATA[ + export BF_MAX_MEM="\${GALAXY_MEMORY_MB}m" && + mkdir -p '${output.files_path}/A/0' && + ln -sf '$image' '${output.files_path}/A/0/image01.ome.tiff' && + #if $masks + info=\$(showinf -nopix -nometa -noflat '${output.files_path}/A/0/image01.ome.tiff') && + echo '>showinf -nopix -nometa -noflat \$image' && + echo "\$info\n" && + masks_info=\$(showinf -nopix -nometa -noflat '$masks') && + echo '>showinf -nopix -nometa -noflat \$masks' && + echo "\$masks_info\n" && + masks_n_resolutions=\$(echo "\$masks_info" | grep '^\s*Resolutions\s*=' -m1 | cut -d'=' -f2 | xargs) && + if [ -z \$masks_n_resolutions ]; then + n_resolutions=\$(echo "\$info" | grep '^\s*Resolutions\s*=' -m1 | cut -d'=' -f2 | xargs) && + pyramid_scale=1 && + if [ -z "\$n_resolutions" ]; then + echo "Warning: Failded to retrieve the number of pyramid resolutions. Set pyramid resolutions to 4 and scale to 2!"; + n_resolutions=4; + pyramid_scale=2; + else + echo "Found the number of pyramid resolutions: \$n_resolutions"; + if [ "\$n_resolutions" -gt 1 ]; then + sizeX0=\$(echo "\$info" | grep '^\s*sizeX\[0\]\s*=' -m1 | cut -d'=' -f2 | xargs) ; + sizeX1=\$(echo "\$info" | grep '^\s*sizeX\[1\]\s*=' -m1 | cut -d'=' -f2 | xargs) ; + if [ "\$sizeX0" -gt 0 ] && [ "\$sizeX1" -gt 0 ]; then + pyramid_scale=\$(((\$sizeX0 + \$sizeX1 / 2 ) / \$sizeX1)); + echo "Calculate pyramid scale: \$sizeX0 / \$sizeX1 ~= \$pyramid_scale."; + else + pyramid_scale=2; + echo "Warning: Failed to calculate the pyramid scale; set it to 2!"; + fi; + fi; + fi; + tile_info=\$(showinf -nopix -nometa -noflat '${output.files_path}/A/0/image01.ome.tiff' | grep '^\s*Tile\ssize\s*=' -m1); + tile_x=\$(echo "\$tile_info" | cut -d' ' -f4); + tile_y=\$(echo "\$tile_info" | cut -d' ' -f6); + convert_cmd="bfconvert -pyramid-resolutions \$n_resolutions -pyramid-scale \$pyramid_scale -noflat -tilex \$tile_x -tiley \$tile_y '$masks' '${output.files_path}/A/0/masks01.ome.tiff'"; + echo "\n>\$convert_cmd"; + eval \$convert_cmd; + masks_info_new=\$(showinf -nopix -nometa -noflat '${output.files_path}/A/0/masks01.ome.tiff'); + echo "\n>showinf -nopix -nometa -noflat '${output.files_path}/A/0/masks01.ome.tiff'"; + echo "\$masks_info_new\n"; + else + ln -sf '$masks' '${output.files_path}/A/0/masks01.ome.tiff'; + fi && + #end if + python '$__tool_directory__/@TOOL_ID@.py' + --inputs '$inputs' + --output '${output.files_path}' + --image '${output.files_path}/A/0/image01.ome.tiff' + #if $masks + --masks '${output.files_path}/A/0/masks01.ome.tiff' + #end if + #if $do_phenotyping.phenotyping_choice + --anndata '$anndata' + #end if + && + cp -R '$__tool_directory__/static' '${output.files_path}' && + cp '$__tool_directory__/index.html' '$output'; + + ]]> + </command> + </xml> + +</macros> |
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| diff -r 000000000000 -r 9f60ef2d586e static/css/2.f290e260.chunk.css --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/static/css/2.f290e260.chunk.css Thu Sep 08 17:23:33 2022 +0000 |
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| diff -r 000000000000 -r 9f60ef2d586e static/css/2.f290e260.chunk.css.map --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/static/css/2.f290e260.chunk.css.map Thu Sep 08 17:23:33 2022 +0000 |
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| diff -r 000000000000 -r 9f60ef2d586e static/css/main.a53cc462.chunk.css --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/static/css/main.a53cc462.chunk.css Thu Sep 08 17:23:33 2022 +0000 |
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| @@ -0,0 +1,163 @@ +/* +object-assign +(c) Sindre Sorhus +@license MIT +*/ + +/* Copyright 2015-2018 Esri. Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 @preserve */ + +/*! + Copyright (c) 2017 Jed Watson. + Licensed under the MIT License (MIT), see + http://jedwatson.github.io/classnames + */ + +/*! + Copyright (c) 2017 Jed Watson. + Licensed under the MIT License (MIT), see + http://jedwatson.github.io/classnames +*/ + +/*! + * The buffer module from node.js, for the browser. + * + * @author Feross Aboukhadijeh <http://feross.org> + * @license MIT + */ + +/*! + * https://github.com/Starcounter-Jack/JSON-Patch + * (c) 2017 Joachim Wester + * MIT license + */ + +/*! ***************************************************************************** +Copyright (c) Microsoft Corporation. + +Permission to use, copy, modify, and/or distribute this software for any +purpose with or without fee is hereby granted. + +THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH +REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY +AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, +INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM +LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR +OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR +PERFORMANCE OF THIS SOFTWARE. +***************************************************************************** */ + +/*! Hammer.JS - v2.0.7 - 2016-04-22 + * http://hammerjs.github.io/ + * + * Copyright (c) 2016 Jorik Tangelder; + * Licensed under the MIT license */ + +/** + * splaytree v3.1.0 + * Fast Splay tree for Node and browser + * + * @author Alexander Milevski <info@w8r.name> + * @license MIT + * @preserve + */ + +/** + * @license Complex.js v2.0.11 11/02/2016 + * + * Copyright (c) 2016, Robert Eisele (robert@xarg.org) + * Dual licensed under the MIT or GPL Version 2 licenses. + **/ + +/** + * @license Fraction.js v4.0.12 09/09/2015 + * http://www.xarg.org/2014/03/rational-numbers-in-javascript/ + * + * Copyright (c) 2015, Robert Eisele (robert@xarg.org) + * Dual licensed under the MIT or GPL Version 2 licenses. + **/ + +/** + * @license long.js (c) 2013 Daniel Wirtz <dcode@dcode.io> + * Released under the Apache License, Version 2.0 + * see: https://github.com/dcodeIO/long.js for details + */ + +/** + * A better abstraction over CSS. + * + * @copyright Oleg Isonen (Slobodskoi) / Isonen 2014-present + * @website https://github.com/cssinjs/jss + * @license MIT + */ + +/** @license React v0.19.1 + * scheduler.production.min.js + * + * Copyright (c) Facebook, Inc. and its affiliates. + * + * This source code is licensed under the MIT license found in the + * LICENSE file in the root directory of this source tree. + */ + +/** @license React v16.13.0 + * react-is.production.min.js + * + * Copyright (c) Facebook, Inc. and its affiliates. + * + * This source code is licensed under the MIT license found in the + * LICENSE file in the root directory of this source tree. + */ + +/** @license React v16.14.0 + * react-dom.production.min.js + * + * Copyright (c) Facebook, Inc. and its affiliates. + * + * This source code is licensed under the MIT license found in the + * LICENSE file in the root directory of this source tree. + */ + +/** @license React v16.14.0 + * react-jsx-dev-runtime.production.min.js + * + * Copyright (c) Facebook, Inc. and its affiliates. + * + * This source code is licensed under the MIT license found in the + * LICENSE file in the root directory of this source tree. + */ + +/** @license React v16.14.0 + * react.production.min.js + * + * Copyright (c) Facebook, Inc. and its affiliates. + * + * This source code is licensed under the MIT license found in the + * LICENSE file in the root directory of this source tree. + */ + +/** @license URI.js v4.2.1 (c) 2011 Gary Court. License: http://github.com/garycourt/uri-js */ + +/**! + * @fileOverview Kickass library to create and place poppers near their reference elements. + * @version 1.16.1-lts + * @license + * Copyright (c) 2016 Federico Zivolo and contributors + * + * Permission is hereby granted, free of charge, to any person obtaining a copy + * of this software and associated documentation files (the "Software"), to deal + * in the Software without restriction, including without limitation the rights + * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the Software is + * furnished to do so, subject to the following conditions: + * + * The above copyright notice and this permission notice shall be included in all + * copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE + * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, + * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE + * SOFTWARE. + */ |
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| diff -r 000000000000 -r 9f60ef2d586e static/media/menu.bc56e94a.svg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/static/media/menu.bc56e94a.svg Thu Sep 08 17:23:33 2022 +0000 |
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| diff -r 000000000000 -r 9f60ef2d586e test-data/cropped_reactive_core.ome.tiff |
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| diff -r 000000000000 -r 9f60ef2d586e test-data/tutorial_vitessce.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tutorial_vitessce.html Thu Sep 08 17:23:33 2022 +0000 |
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| @@ -0,0 +1,39 @@ +<!doctype html> +<html lang="en"> + <head> + <meta charset="utf-8"> + <style> + body,html{height:100%} + body{ + font-family:-apple-system,'Helvetica Neue',Arial,sans-serif;display:flex;flex-direction:column} + #full-app{flex:1} + #full-app .vitessce-container{ + height:max(100%,100vh);width:100%;overflow:hidden} + #full-app #small-app .vitessce-container{height:600px} + </style> + <title>Vitessce</title> + <link href="./static/css/2.f290e260.chunk.css" rel="stylesheet"> + <link href="./static/css/main.a53cc462.chunk.css" rel="stylesheet"> + </head> + <body> + <div id="full-app"> + <div class="container-fluid"> + <div class="row p-2"> + <div class="col col-full"> + <h1>Vitessce is loading...</h1> + <div style="width:1000px"> + <div id="small-app"> + </div> + </div> + </div> + </div> + </div> + </div> + <noscript>You need to enable JavaScript to run this app.</noscript> + <script> + !function(e){function t(t){for(var n,i,l=t[0],f=t[1],a=t[2],p=0,s=[];p<l.length;p++)i=l[p],Object.prototype.hasOwnProperty.call(o,i)&&o[i]&&s.push(o[i][0]),o[i]=0;for(n in f)Object.prototype.hasOwnProperty.call(f,n)&&(e[n]=f[n]);for(c&&c(t);s.length;)s.shift()();return u.push.apply(u,a||[]),r()}function r(){for(var e,t=0;t<u.length;t++){for(var r=u[t],n=!0,l=1;l<r.length;l++){var f=r[l];0!==o[f]&&(n=!1)}n&&(u.splice(t--,1),e=i(i.s=r[0]))}return e}var n={},o={1:0},u=[];function i(t){if(n[t])return n[t].exports;var r=n[t]={i:t,l:!1,exports:{}};return e[t].call(r.exports,r,r.exports,i),r.l=!0,r.exports}i.m=e,i.c=n,i.d=function(e,t,r){i.o(e,t)||Object.defineProperty(e,t,{enumerable:!0,get:r})},i.r=function(e){"undefined"!=typeof Symbol&&Symbol.toStringTag&&Object.defineProperty(e,Symbol.toStringTag,{value:"Module"}),Object.defineProperty(e,"__esModule",{value:!0})},i.t=function(e,t){if(1&t&&(e=i(e)),8&t)return e;if(4&t&&"object"==typeof e&&e&&e.__esModule)return e;var r=Object.create(null);if(i.r(r),Object.defineProperty(r,"default",{enumerable:!0,value:e}),2&t&&"string"!=typeof e)for(var n in e)i.d(r,n,function(t){return e[t]}.bind(null,n));return r},i.n=function(e){var t=e&&e.__esModule?function(){return e.default}:function(){return e};return i.d(t,"a",t),t},i.o=function(e,t){return Object.prototype.hasOwnProperty.call(e,t)},i.p="./";var l=this.webpackJsonpvitessce=this.webpackJsonpvitessce||[],f=l.push.bind(l);l.push=t,l=l.slice();for(var a=0;a<l.length;a++)t(l[a]);var c=f;r()}([]) + </script> + <script src="./static/js/2.eb2fd6ea.chunk.js"></script> + <script src="./static/js/main.303f671d.chunk.js"></script> + </body> +</html> \ No newline at end of file |
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| diff -r 000000000000 -r 9f60ef2d586e vitessce_spatial.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/vitessce_spatial.py Thu Sep 08 17:23:33 2022 +0000 |
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| @@ -0,0 +1,121 @@ +import argparse +import json +import warnings +from pathlib import Path + +import scanpy as sc +from anndata import read_h5ad +from vitessce import ( + AnnDataWrapper, + Component as cm, + MultiImageWrapper, + OmeTiffWrapper, + VitessceConfig, +) + + +def main(inputs, output, image, anndata=None, masks=None): + """ + Parameter + --------- + inputs : str + File path to galaxy tool parameter. + output : str + Output folder for saving web content. + image : str + File path to the OME Tiff image. + anndata : str + File path to anndata containing phenotyping info. + masks : str + File path to the image masks. + """ + warnings.simplefilter('ignore') + + with open(inputs, 'r') as param_handler: + params = json.load(param_handler) + + vc = VitessceConfig(name=None, description=None) + dataset = vc.add_dataset() + image_wrappers = [OmeTiffWrapper(img_path=image, name='OMETIFF')] + if masks: + image_wrappers.append( + OmeTiffWrapper(img_path=masks, name='MASKS', is_bitmask=True) + ) + dataset.add_object(MultiImageWrapper(image_wrappers)) + + status = vc.add_view(dataset, cm.STATUS) + spatial = vc.add_view(dataset, cm.SPATIAL) + lc = vc.add_view(dataset, cm.LAYER_CONTROLLER) + + if not anndata: + vc.layout(status / lc | spatial) + config_dict = vc.export(to='files', base_url='http://localhost', out_dir=output) + with open(Path(output).joinpath('config.json'), 'w') as f: + json.dump(config_dict, f, indent=4) + return + + adata = read_h5ad(anndata) + + params = params['do_phenotyping'] + embedding = params['scatterplot_embeddings']['embedding'] + embedding_options = params['scatterplot_embeddings']['options'] + if embedding == 'umap': + sc.pp.neighbors(adata, **embedding_options) + sc.tl.umap(adata) + mappings_obsm = 'X_umap' + mappings_obsm_name = "UMAP" + elif embedding == 'tsne': + sc.tl.tsne(adata, **embedding_options) + mappings_obsm = 'X_tsne' + mappings_obsm_name = "tSNE" + else: # pca + sc.tl.pca(adata, **embedding_options) + mappings_obsm = 'X_pca' + mappings_obsm_name = "PCA" + + adata.obsm['XY_centroid'] = adata.obs[['X_centroid', 'Y_centroid']].values + + cell_set_obs = params['phenotype_factory']['phenotypes'] + if not isinstance(cell_set_obs, list): + cell_set_obs = [x.strip() for x in cell_set_obs.split(',')] + cell_set_obs_names = [obj[0].upper() + obj[1:] for obj in cell_set_obs] + dataset.add_object( + AnnDataWrapper( + adata, + mappings_obsm=[mappings_obsm], + mappings_obsm_names=[mappings_obsm_name], + spatial_centroid_obsm='XY_centroid', + cell_set_obs=cell_set_obs, + cell_set_obs_names=cell_set_obs_names, + expression_matrix="X" + ) + ) + + cellsets = vc.add_view(dataset, cm.CELL_SETS) + scattorplot = vc.add_view(dataset, cm.SCATTERPLOT, mapping=mappings_obsm_name) + heatmap = vc.add_view(dataset, cm.HEATMAP) + genes = vc.add_view(dataset, cm.GENES) + cell_set_sizes = vc.add_view(dataset, cm.CELL_SET_SIZES) + cell_set_expression = vc.add_view(dataset, cm.CELL_SET_EXPRESSION) + vc.layout( + (status / genes / cell_set_expression) + | (cellsets / lc / scattorplot) + | (cell_set_sizes / heatmap / spatial) + ) + config_dict = vc.export(to='files', base_url='http://localhost', out_dir=output) + + with open(Path(output).joinpath('config.json'), 'w') as f: + json.dump(config_dict, f, indent=4) + + +if __name__ == '__main__': + aparser = argparse.ArgumentParser() + aparser.add_argument("-i", "--inputs", dest="inputs", required=True) + aparser.add_argument("-e", "--output", dest="output", required=True) + aparser.add_argument("-g", "--image", dest="image", required=True) + aparser.add_argument("-a", "--anndata", dest="anndata", required=False) + aparser.add_argument("-m", "--masks", dest="masks", required=False) + + args = aparser.parse_args() + + main(args.inputs, args.output, args.image, args.anndata, args.masks) |
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| diff -r 000000000000 -r 9f60ef2d586e vitessce_spatial.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/vitessce_spatial.xml Thu Sep 08 17:23:33 2022 +0000 |
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| b'@@ -0,0 +1,142 @@\n+<tool id="vitessce_spatial" name="Vitessce Visualization" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">\n+ <description>integrative visualization of multi-modal, spatial single-cell data</description>\n+\n+ <macros>\n+ <import>main_macros.xml</import>\n+ </macros>\n+\n+ <expand macro="vitessce_requirements"/>\n+ <expand macro="macro_stdio" />\n+ <version_command> "@VERSION@"</version_command>\n+ <expand macro="vitessce_cmd" />\n+\n+ <configfiles>\n+ <inputs name="inputs" />\n+ </configfiles>\n+\n+ <inputs>\n+ <param name="image" type="data" format="ome.tiff" label="Select the OME Tiff image" />\n+ <param name="masks" type="data" format="tiff,ome.tiff" optional="true" label="Select masks for the OME Tiff image (Optional)" />\n+ <conditional name="do_phenotyping">\n+ <param name="phenotyping_choice" type="boolean" checked="true" label="Whether to do phenotyping">\n+ </param>\n+ <when value="true">\n+ <param name="anndata" type="data" format="h5ad" label="Select the anndata contaning phenotyping info" />\n+ <conditional name="scatterplot_embeddings">\n+ <param name="embedding" type="select" label="Select an embedding algorithm for scatterplot">\n+ <option value="umap" selected="true">UMAP</option>\n+ <option value="tsne">tSNE</option>\n+ <option value="pca">PCA</option>\n+ </param>\n+ <when value="umap">\n+ <section name="options" title="Advance Options for neighbor search">\n+ <param argument="n_neighbors" type="integer" value="30" label="The size of local neighborhood used for manifold approximation" />\n+ <param argument="n_pcs" type="integer" value="10" label="Number of PCs" />\n+ <param argument="knn" type="boolean" checked="true" label="Whether to use knn graph" help="If false, use a Gaussian Kernel to assign low weights to neighbors more distant than the n_neighbors nearest neighbor." />\n+ <param argument="random_state" type="integer" value="0" optional="true" label="Randomness seed" />\n+ </section>\n+ </when>\n+ <when value="tsne">\n+ <section name="options" title="Advance Options for computing tSNE">\n+ <param argument="n_pcs" type="integer" value="10" label="Number of PCs" />\n+ <param argument="learning_rate" type="float" value="1000" label="Learning rate" help="Should be 100-1000." />\n+ <param argument="random_state" type="integer" value="0" optional="true" label="Randomness seed" />\n+ </section>\n+ </when>\n+ <when value="pca">\n+ <section name="options" title="Advance Options for computing PCA">\n+ <param argument="n_comps" type="integer" value="" optional="true" label="Number of principal components to compute" help="Defaults to 50, or 1 - minimum dimension size of selected representation." />\n+ <param argument="zero_center" type="boolean" checked="true" label="Whether to compute standard PCA from covariance matrix" help="If False, omit zero-centering variables (uses TruncatedSVD)" />\n+ <param argument="svd_solver" type="select" label="Select the SVD solver">\n+ <option value="arpack" selected="true">arpack</option>\n+ <option value="randomized">randomized</option>\n+ <option value="auto">auto</option>\n+ <option value="lobpcg">lobpcg</option>\n+ </param>\n+ '..b'"integer" value="0" optional="true" label="Randomness seed" />\n+ </section>\n+ </when>\n+ </conditional>\n+ <conditional name="phenotype_factory">\n+ <param name="phenotype_mode" type="select" label="Input phenotyping keys">\n+ <option value="choices" selected="true">Multiple choices</option>\n+ <option value="type_in">Type in</option>\n+ </param>\n+ <when value="choices">\n+ <param name="phenotypes" type="select" multiple="true" display="checkboxes" label="Select the key(s)" >\n+ <option value="phenotype" selected="true">\'phenotype\' (via scimap phenotyping)</option>\n+ <option value="kmeans">\'kmeans\' (via clustering)</option>\n+ <option value="leiden">\'leiden\' (via clustering)</option>\n+ <option value="phenograph">\'phenograph\' (via clustering)</option>\n+ <option value="parc">\'parc\' (via clustering)</option>\n+ </param>\n+ </when>\n+ <when value="type_in">\n+ <param name="phenotypes" type="text" value="" label="Type in the keys storing phenotypes" help="Comma delimited for multiple keys."/>\n+ </when>\n+ </conditional>\n+ </when>\n+ <when value="false">\n+ </when>\n+ </conditional>\n+ </inputs>\n+ <outputs>\n+ <data format="html" name="output" />\n+ </outputs>\n+ <tests>\n+ <test>\n+ <param name="image" value="cropped_reactive_core.ome.tiff" ftype="ome.tiff" />\n+ <conditional name="do_phenotyping">\n+ <param name="phenotyping_choice" value="yes" />\n+ <param name="anndata" value="cropped_tutorial_data_pheno.h5ad" ftype="h5ad" />\n+ <conditional name="phenotype_factory">\n+ <param name="phenotype_mode" value="type_in" />\n+ <param name="phenotypes" value="leiden" />\n+ </conditional>\n+ </conditional>\n+ <output name="output" file="tutorial_vitessce.html" compare="sim_size" delta="20" />\n+ </test>\n+ <test>\n+ <param name="image" value="cropped_reactive_core.ome.tiff" ftype="ome.tiff" />\n+ <conditional name="do_phenotyping">\n+ <param name="phenotyping_choice" value="yes" />\n+ <param name="anndata" value="cropped_tutorial_data_pheno.h5ad" ftype="h5ad" />\n+ <conditional name="scatterplot_embeddings">\n+ <param name="embedding" value="pca" />\n+ </conditional>\n+ <conditional name="phenotype_factory">\n+ <param name="phenotype_mode" value="type_in" />\n+ <param name="phenotypes" value="leiden" />\n+ </conditional>\n+ </conditional>\n+ <output name="output" file="tutorial_vitessce.html" compare="sim_size" delta="20" />\n+ </test>\n+ <test>\n+ <param name="image" value="cropped_reactive_core.ome.tiff" ftype="ome.tiff" />\n+ <conditional name="do_phenotyping">\n+ <param name="phenotyping_choice" value="no" />\n+ </conditional>\n+ <output name="output" file="tutorial_vitessce.html" compare="sim_size" delta="20" />\n+ </test>\n+ </tests>\n+ <help>\n+ <![CDATA[\n+**What it does**\n+This tools provides web-based, interactive and scalable visualizations of single cell data.\n+\n+**Input**\n+\n+OME-TIFF image.\n+Segmentation masks (optional).\n+AnnData with marker intensities.\n+\n+**Output**\n+\n+An HTML file with Vitessce component. \n+\n+ ]]>\n+ </help>\n+ <citations>\n+ <citation type="doi">10.31219/osf.io/y8thv</citation>\n+ </citations>\n+</tool>\n' |
