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* Switch logic from `--annotations` to `--disable-annotations * Rename `--annotations-file` --> `--annotations-input-file` and remove `experimental` * update docs * update makefile * update tests * Disable annotations on standard client smoke test * Update docs/posts/annotations.md Co-Authored-By: Matt Weiden <538456+mweiden@users.noreply.github.com> * Update docs/posts/annotations.md * Renaming * Docs * Update tests * Pesky typo -_- Co-authored-by: Matt Weiden <538456+mweiden@users.noreply.github.com>
78 lines
3.6 KiB
Markdown
78 lines
3.6 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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cellxgene 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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`--disable-annotations`, `--annotations-file` & `--annotations-dir` all have to do with creating new categorical annotations in the application. We have a [whole separate page](annotations) about their usage! :)
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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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