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Rename "layout" to "embedding" in the UI (#921)

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* rename "layout" to "embedding" in the UI

* docs changes for layout

* fix typo in data docs

* new help text, per PR review
This commit is contained in:
Bruce Martin
2019-09-16 15:34:14 -07:00
committed by GitHub
parent ec4da63408
commit 922c375333
7 changed files with 39 additions and 33 deletions
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docs/faq.md
+3 -3
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@@ -21,13 +21,13 @@ The output of `cellxgene prepare` is a h5ad file with your computed clusters and
Yep! This should only take a couple steps. We'll assume your data is in a folder called `data/` and you've successfully installed `cellxgene` with the `prepare` packages as described above. Just run
```
cellxgene prepare data/ --output=data-processed.h5ad --layout=umap
cellxgene prepare data/ --output=data-processed.h5ad --embedding=umap
```
Depending on the size of the dataset, this may take some time. Once it's done, call
```
cellxgene launch data-processed.h5ad --layout=umap --open
cellxgene launch data-processed.h5ad --embedding=umap --open
```
And your web browser should open with an interactive view of your data.
@@ -40,7 +40,7 @@ Currently this is not supported directly, but you should be able to do this your
- `.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. If an embedding has more than two components, the first two will be used for visualization.
- `.obsm` is used for embedding(s). If an embedding has more than two components, the first two will be used for visualization.
#### I have a BIG dataset - how can I make cellxgene run as fast as possible?