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Merge branch 'master' of https://github.com/chanzuckerberg/cellxgene into bkmartinjr-crossfiltergroups

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bkmartinjr
2018-08-07 13:52:12 -07:00
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111
README.md
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@@ -21,41 +21,108 @@ Started in the context of the Human Cell Atlas Consortium, cellxgene hopes to bo
- OS: OSX, Windows, Linux
- python 3.6
- npm
- Google Chrome
- Google Chrome
**Clone project**
git clone https://github.com/chanzuckerberg/cellxgene.git
**Clone project**
git clone https://github.com/chanzuckerberg/cellxgene.git
**Install client**
**Install client**
cd cellxgene
./bin/build-client
./bin/build-client
**To use with virtual env for python**
(optional, but recommended)
ENV_NAME=cellxgene
python3 -m venv ${ENV_NAME}
source ${ENV_NAME}/bin/activate
**To use with virtual env for python**
(optional, but recommended)
**Install server**
pip install -e .
ENV_NAME=cellxgene
python3 -m venv ${ENV_NAME}
source ${ENV_NAME}/bin/activate
**Install server**
pip install -e .
**Run (with demo data)**
**Run (with demo data)**
cellxgene --title PBMC3K scanpy example-dataset/
*In google chrome, navigate to the viewer via the web address printed in your console.
*In google chrome, navigate to the viewer via the web address printed in your console.
E.g.,* `Running on http://0.0.0.0:5005/`
**Help**
cellxgene --help
_For help with the scanpy engine_
_For help with the scanpy engine_
cellxgene scanpy --help
## Using your own data
### Scanpy
To prepare your data you will need to format your data into AnnData format using scanpy and calculate PCA and nearest neighbors and save in h5ad format.
1. [Load data into scanpy](https://scanpy.readthedocs.io/en/latest/api/index.html#reading)
- Ensure that `obs`'s index is the cell names: `print(data.obs_names)` should show your cell indices. If it shows gene names, you may need to just call `data.transpose()`.
2. Calculate PCA
sc.pp.pca(data) ## sc is scanpy.api
3. Calculate nearest neighbors (depending on layout algorithm)
```
# For umap layout algorithm, you need to use the "umap" method for neighbors
sc.pp.neighbors(data, method="umap", metric="euclidean", use_rep="X_pca")
# For tsne layout algorithm, you can use either "umap" or "gauss"; we recommend "gauss"
sc.pp.neighbors(data, method="gauss", metric="euclidean", use_rep="X_pca")
```
4. Save file
```
# cellxgene requires file to be named data.h5ad
data.write("data.h5ad")
```
5. Create config file (optional)
If you do not have a config file, the schema (metadata names, types, and categorical/continuous) will be inferred from the observations in the data file. Config file is required to be named 'data_schema.json' and located in the same directory as data file.
- The config file is a JSON format file with information on the metadata associated with the cells. The key is the column name in obs. The value is an object
```
type: string, int, or float (what type the values are),
variabletype: categorical or continuous (categorical values are displayed as checkboxes, continuous values are displayed as a histogram)
displayname: (what the heading should be displayed as)
include: True/False (whether to display values on web interface)
```
```
Example
{
"CellName": {
"type": "string",
"variabletype": "categorical",
"displayname": "Name",
"include": true
},
"clusters": {
"type": "string",
"variabletype": "categorical",
"displayname": "Clusters",
"include": true
},
"num_genes": {
"type": "int",
"variabletype": "continuous",
"displayname": "Number Genes",
"include": true
}
}
```
## Contributing
We warmly welcome contributions from the community. Please submit any bug reports and feature requests through github issues. Please submit any direct contributions via a branch + pull request.

12
client/package.json
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@@ -2,6 +2,7 @@
"name": "cellxgene",
"version": "0.0.1",
"license": "MIT",
"description": "cellxgene is a web application for the interactive exploration of single cell sequence data.",
"repository": "https://github.com/chanzuckerberg/cellxgene",
"scripts": {
"build": "npm run clean && webpack --config configuration/webpack/webpack.config.prod.js",
@@ -29,16 +30,13 @@
"dependencies": {
"canvas-fit": "^1.5.0",
"d3": "^4.10.0",
"deck.gl": "^4.1.2",
"express": "^4.14.0",
"font-color-contrast": "^1.0.3",
"gl-mat4": "^1.1.4",
"gl-matrix": "^2.7.1",
"halogen": "^0.2.0",
"hsv2rgb": "^1.1.0",
"key-pressed": "0.0.1",
"lodash": "^4.17.4",
"luma.gl": "^4.0.3",
"mouse-position": "^2.0.1",
"mouse-pressed": "^1.0.0",
"orbit-camera": "^1.0.0",
@@ -50,7 +48,6 @@
"react-hot-loader": "^3.0.0-beta.7",
"react-icons": "^2.2.7",
"react-redux": "^5.0.6",
"react-router-dom": "4.1.2",
"redux": "^3.7.2",
"redux-thunk": "^2.2.0",
"regl": "^1.3.1",
@@ -81,12 +78,12 @@
"cross-env": "^3.1.4",
"css-loader": "^0.26.1",
"css-modules-require-hook": "^4.0.1",
"enzyme": "^2.4.1",
"enzyme": "^3.3.0",
"eslint": "^4.18.2",
"eslint-loader": "^1.5.0",
"eslint-plugin-filenames": "^1.1.0",
"eslint-plugin-import": "^2.2.0",
"eslint-plugin-jsx-a11y": "^3.0.2",
"eslint-plugin-jsx-a11y": "^6.1.1",
"eslint-plugin-react": "^6.0.0",
"extract-text-webpack-plugin": "^2.0.0-beta.3",
"file-loader": "^0.9.0",
@@ -97,7 +94,8 @@
"jest": "^23.4.1",
"jsdom": "^9.4.1",
"json-loader": "^0.5.4",
"nyc": "^10.0.0",
"nyc": "^13.0.1",
"postcss": "^6.0.0",
"postcss-loader": "^1.2.2",
"promise": "^7.1.1",
"react-addons-test-utils": "^15.3.0",