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78 lines
3.9 KiB
Markdown
78 lines
3.9 KiB
Markdown
---
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layout: default
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title: demo-data
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description: Demo datasets
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---
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# Launching cellxgene with your dataset
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## Quickstart
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Once you've [prepared your data](prepare) for cellxgene, you can launch the app using
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```
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cellgene launch mydataset.h5ad --open
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```
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You should see your web browser open with the following
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<img width="450" src="https://raw.githubusercontent.com/chanzuckerberg/cellxgene/master/docs/cellxgene-opening-screenshot.png" pad="50px">
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**Note**: automatic opening of the browser with the `--open` flag only works on some platforms (eg, OSX). On other platforms you'll need to directly point to the provided link in your browser.
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## Launching from a URL
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You can also launch from a URL directly like this:
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```
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cellxgene launch https://github.com/chanzuckerberg/cellxgene/blob/master/example-dataset/pbmc3k.h5ad
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```
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Support for S3 and GCS is not enabled by default. If you wish to directly access S3 or GFS, install one or both of the following packages:
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- [s3fs](https://s3fs.readthedocs.io/en/latest/) for S3 support
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- [gcsfs](https://gcsfs.readthedocs.io/en/latest/) for GCS support
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For example:
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```
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pip install s3fs
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cellxgene launch s3://mybucket.s3-us-west-2.amazonaws.com/mydata.h5ad
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```
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## Options for cellxgene `launch`
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**For the most up-to-date and comprehensive list of options, run `cellxgene launch --help`**
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`--open` automatically opens the web browser after launching (caveat: only works on some operating systems).
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`--experimental-label-file` enables an experimental feature to allow users to create new categorical annotations in the application. These newly-created annotations are saved in the specified CSV file. If the specified file already exists, the previously-contained annotations will be loaded as mutable (changeable) values and the CSV will be updated (overwritten) with any edits made. If the file does not exist, it will be created. See [the annotations documentation](annotations) for more details.
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`--diffexp-lfc-cutoff` as explained [in the methods](methods), genes are only returned in differential expression if the effect size is above the specified threshold for log fold change. Defaults to 0.01.
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`--disable-diffexp` will disable and hide the `Compute Differential Expression` feature.
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For large datasets, or datasets loaded with the `--backed` option, computing differential expression may
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be extremely slow or use excessive resources on the host computer (e.g., memory thrashing).
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Disabling the feature will ensure that this computation is not initiated accidentally.
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`--backed` option instructs `cellxgene launch` to read the H5AD file in "backed" mode (for more information, see the
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[anndata.read_h5ad() documentation](https://anndata.readthedocs.io/en/latest/anndata.read_h5ad.html#anndata.read_h5ad)).
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By default, cellxgene will read the entire H5AD will be into memory at startup, improving application speed and performance.
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Very large datasets may not fit in memory. The "--backed" mode will read the file incrementally, reducing memory
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use, and for large files, improving startup speed. _However_, this option will also significantly slow
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down access to gene expression histograms, and may render differential expression calculations too slow
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to use (see `--disable-diffexp` for an option to disable this feature).
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`--embedding` restricts which embeddings will be available in the viewer. By default, all embeddings specified in `anndata.obsm['X_name']` will be loaded; if you have many embeddings, you may wish to restrict this list for a speedier launch.
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`--title` adds a title to the viewer. Defaults to file name.
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`--about` adds a link where users can go to find more infomation about the dataset. Requires `https`.
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`--obs-names` allows you to specify which column in `anndata.obs` to use as `anndata.obs.index`.
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`--var-names` allows you to specify which column in `anndata.var` to use as `anndata.var.index`.
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`--max-category-items` omits categorical metadata fields that contain more than N _distinct_ values. Defaults to 1000.
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