fork/cellxgene
1
0
Fork 0
mirror of https://github.com/chanzuckerberg/cellxgene.git synced 2026-10-02 14:58:12 +08:00
Code Issues Packages Projects Releases Wiki Activity

Add support for anndata backed mode (#943)

Browse Source 
* initial cut at backed mode

* make flask multithreading conditional on debug flag

* update X access to support backed mode

* lint

* improve help message for backed mode

* fix tests

* add MatrixProxy to normalize supported matrix types

* add FAQ entry for --backed

* remove use of matrix.T

* clean up

* add ability to disable diffexp from CLI; add hueristic to detect likely slow diffexp calculation, and warn user

* fix tests

* do not print diffexp speed warning if diffexp is disabled

* tweak wording of diffexp speed messages

* add FAQ entry on --disable-diffexp

* revise heuristic for warning about slow diffexp

* use quick tooltip delay on diffexp button
This commit is contained in:
Bruce Martin
2019-10-08 11:16:07 -07:00
committed by GitHub
parent 1467357db5
commit 711f3b7048
15 changed files with 881 additions and 99 deletions
Download Patch File Download Diff File Expand all files Collapse all files
docs/faq.md
+19 -1
View File
@@ -12,7 +12,7 @@ Currently, you can go straight into `cellxgene launch` with your own analyzed da
If your data is in a different format, and/or you still need to perform dimensionality reduction and clustering, `cellxgene` can do that for you with the `prepare` command. `cellxgene prepare` runs `scanpy` under the hood and can read in any format that is currently supported by `scanpy` (including mtx, loom, and more listed [here](https://scanpy.readthedocs.io/en/latest/api/index.html#reading)).
To add `cellxgene prepare` to your cellxgene installation run `pip install cellxgene[prepare]`.
To add `cellxgene prepare` to your cellxgene installation run `pip install cellxgene[prepare]`.
The output of `cellxgene prepare` is a h5ad file with your computed clusters and tsne/umap projections that can be used in `cellxgene launch`.
@@ -110,3 +110,21 @@ For example:
pip install s3fs
cellxgene launch s3://mybucket.s3-us-west-2.amazonaws.com/mydata.h5ad
```
#### What does the command line option `--backed` do?
The `--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).
#### What does the command line option `--disable-diffexp` do?
The `--disable-diffexp` option 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 reources on the host computer (eg, memory thrasing).
Disabling the feature will ensure that the end-user does not accidentally initiate this computation.