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add FAQs to readme (#482)

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Added question and answer to FAQ; added link to scanpy documentation on scientific recipes.
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fionagriffin
2018-11-29 13:59:10 -08:00
committed by Charlotte Weaver
parent 76c0cbf16b
commit a83ec60308
1 changed files with 7 additions and 1 deletions
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README.md
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@@ -68,7 +68,7 @@ To prepare from an existing `.h5ad` file use
cellxgene prepare dataset.h5ad --output=dataset-processed.h5ad
```
This will load the input data, perform PCA and nearest neighbor calculations, compute `umap` and `tsne` layouts and `louvain` cluster assignments, and save the results in a new file called `dataset-processed.h5ad` that can be loaded using `cellxgene launch`. Data can be loaded from several formats, including `.h5ad` `.loom` and a `10-Genomics-formatted` `mtx` directory. Several options are available, including running one of the preprocessing `recipes` included with `scanpy`, which include steps like cell filtering and gene selection.
This will load the input data, perform PCA and nearest neighbor calculations, compute `umap` and `tsne` layouts and `louvain` cluster assignments, and save the results in a new file called `dataset-processed.h5ad` that can be loaded using `cellxgene launch`. Data can be loaded from several formats, including `.h5ad` `.loom` and a `10-Genomics-formatted` `mtx` directory. Several options are available, including running one of the preprocessing `recipes` included with `scanpy`, which include steps like cell filtering and gene selection. To learn more about the `recipes` please see the `scanpy` [documentation](https://github.com/theislab/scanpy/blob/master/scanpy/preprocessing/recipes.py).
Depending on the options chosen, `prepare` can take a long time to run (a few minutes for datasets with 10-100k cells, up to an hour or more for datasets with >100k cells). If you want `prepare` to run faster we recommend using the `sparse` option and only computing the layout for `umap`, using a call like this
@@ -159,6 +159,12 @@ Currently we use a [Welch's *t*-test](https://en.wikipedia.org/wiki/Welch%27s_t-
This is likely because you do not have node and npm installed, we recommend using [nvm](https://github.com/creationix/nvm) if you're new to using these tools.
> What part of the anndata objects does cellxgene pull in for visualization?
- `.obs` and `.var` annotations are use to extract metadata for filtering
- `.X` is used to display expression (histograms, scatterplot & colorscale) and to compute differential expression
- `.obsm` is used for layout
## developer guide
This project has made a few key design choices