--- layout: default title: demo-data description: Demo datasets --- # Launching cellxgene with your dataset ## Quickstart Once you've [prepared your data](prepare) for cellxgene, you can launch the app using ``` cellxgene launch mydataset.h5ad --open ``` You should see your web browser open with the following **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. ## Launching from a URL You can also launch from a URL directly like this: ``` cellxgene launch https://github.com/chanzuckerberg/cellxgene/blob/main/example-dataset/pbmc3k.h5ad ``` 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: - [s3fs](https://s3fs.readthedocs.io/en/latest/) for S3 support - [gcsfs](https://gcsfs.readthedocs.io/en/latest/) for GCS support For example: ``` pip install s3fs cellxgene launch s3://mybucket.s3-us-west-2.amazonaws.com/mydata.h5ad ``` ## Options for cellxgene `launch` **For the most up-to-date and comprehensive list of options, run `cellxgene launch --help`** `--open` automatically opens the web browser after launching (caveat: only works on some operating systems). `--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! :) `--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. `--disable-diffexp` will disable and hide the `Compute Differential Expression` feature. For large datasets, or datasets loaded with the `--backed` option, computing differential expression may be extremely slow or use excessive resources on the host computer (e.g., memory thrashing). Disabling the feature will ensure that this computation is not initiated accidentally. `--backed` option instructs `cellxgene launch` to read the H5AD file in "backed" mode (for more information, see the [anndata.read_h5ad() documentation](https://anndata.readthedocs.io/en/latest/anndata.read_h5ad.html#anndata.read_h5ad)). By default, cellxgene will read the entire H5AD will be into memory at startup, improving application speed and performance. Very large datasets may not fit in memory. The "--backed" mode will read the file incrementally, reducing memory use, and for large files, improving startup speed. _However_, this option will also significantly slow down access to gene expression histograms, and may render differential expression calculations too slow to use (see `--disable-diffexp` for an option to disable this feature). `--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. `--title` adds a title to the viewer. Defaults to file name. `--about` adds a link where users can go to find more infomation about the dataset. Requires `https`. `--obs-names` allows you to specify which column in `anndata.obs` to use as `anndata.obs.index`. `--var-names` allows you to specify which column in `anndata.var` to use as `anndata.var.index`. `--max-category-items` omits categorical metadata fields that contain more than N _distinct_ values. Defaults to 1000.