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falexwolf committed May 14, 2019
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4 changes: 4 additions & 0 deletions docs/_static/css/custom.css
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77 changes: 32 additions & 45 deletions docs/release_notes.rst
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.. role:: smaller
.. role:: noteversion

On Master :small:`May 7, 2019`
------------------------------

- :func:`~scanpy.pp.calculate_qc_metrics` is now single threaded by default for datasets under 300,000 cells -- allowing cached compilation. See :pr:`615` :smaller:`thanks to I Virshup`

Version 1.4.2 :small:`May 6, 2019`
----------------------------------
Post v1.4 :small:`May 13, 2019`
-------------------------------

New functionality:


- :func:`~scanpy.pp.combat` ComBat function now supports additional covariates which may include adjustment variables or biological condition, see :pr:`618` :smaller:`thanks to G Eraslan`
- :func:`~scanpy.pp.highly_variable_genes` now has a `batch_key` option which performs HVG selection in each batch separately to avoid selecting genes that vary strongly across batches, see :pr:`622` :smaller:`thanks to G Eraslan`

Code design:

- :func:`~scanpy.pp.neighbors` and :func:`~scanpy.tl.umap` got rid of UMAP legacy code and introduced UMAP as a dependency, see :pr:`576` :smaller:`thanks to S Rybakov`
- :func:`~scanpy.pp.combat` supports additional covariates which may include adjustment variables or biological condition :pr:`618` :noteversion:`1.4.2` :smaller:`thanks to G Eraslan`
- :func:`~scanpy.pp.highly_variable_genes` has a `batch_key` option which performs HVG selection in each batch separately to avoid selecting genes that vary strongly across batches :pr:`622` :noteversion:`1.4.2` :smaller:`thanks to G Eraslan`
- Scanpy has a command line interface again. Invoking it with `scanpy somecommand [args]` calls `scanpy-somecommand [args]`, except for builtin commands (currently `scanpy settings`) :pr:`604` :smaller:`thanks to P Angerer`
- :func:`~scanpy.datasets.ebi_expression_atlas` allows convenient download of EBI expression atlas :noteversion:`1.4.1` :smaller:`thanks to I Virshup`
- :func:`~scanpy.tl.marker_gene_overlap` computes overlaps of marker genes :noteversion:`1.4.1` :smaller:`thanks to M Luecken`
- :func:`~scanpy.tl.filter_rank_genes_groups` filters out genes based on fold change and fraction of cells expressing genes :noteversion:`1.4.1` :smaller:`thanks to F Ramirez`
- :func:`~scanpy.pp.normalize_total` replaces :func:`~scanpy.pp.normalize_per_cell`, is more efficient and provides a parameter to only normalize using a fraction of expressed genes :noteversion:`1.4.1` :smaller:`thanks to S Rybakov`
- :func:`~scanpy.pp.downsample_counts` has been sped up, changed default value of `replace` parameter to `False` :pr:`474` :noteversion:`1.4.1` :smaller:`thanks to I Virshup`
- :func:`~scanpy.pl.embedding_density` allows plots of cell densities on embeddings :pr:`543` :noteversion:`1.4.1` :smaller:`thanks to M Luecken`
- :func:`~scanpy.external.palantir` interfaces Palantir [Setty18]_ :pr:`493` :noteversion:`1.4.1` :smaller:`thanks to A Mousa`

Bug fixes:

- :func:`~scanpy.tl.rank_genes_groups` t-test implementation doesn't return NaN when variance is 0, also changed to scipy's implementation, see :pr:`621` :smaller:`thanks to I Virshup`
- :func:`~scanpy.tl.umap` with `init_pos='paga'` detects correct `dtype`
- :func:`~scanpy.tl.louvain` and :func:`~scanpy.tl.leiden` auto-generate `key_added=louvain_R` upon passing `restrict_to`, which was temporarily changed in `v1.4.1`.

- :func:`~scanpy.tl.rank_genes_groups` t-test implementation doesn't return NaN when variance is 0, also changed to scipy's implementation :pr:`621` :noteversion:`1.4.2` :smaller:`thanks to I Virshup`
- :func:`~scanpy.tl.umap` with `init_pos='paga'` detects correct `dtype` :noteversion:`1.4.2` :smaller:`thanks to A Wolf`
- :func:`~scanpy.pp.neighbors` correctly infers `n_neighbors` again from `params`, which was temporarily broken in `v1.4.2` :noteversion:`1.4.3` :smaller:`thanks to I Virshup`
- :func:`~scanpy.tl.louvain` and :func:`~scanpy.tl.leiden` auto-generate `key_added=louvain_R` upon passing `restrict_to`, which was temporarily changed in `v1.4.1` :noteversion:`1.4.2` :smaller:`thanks to A Wolf`

Version 1.4.1 :small:`April 27, 2019`
-------------------------------------

New functionality:

- Scanpy has a command line interface again. Invoking it like ``scanpy somecommand [args]`` simply calls ``scanpy-somecommand [args]``, except for builting commands (currently just ``scanpy settings``). :pr:`604`.
- :func:`~scanpy.datasets.ebi_expression_atlas` allows convenient download of EBI expression atlas :smaller:`thanks to I Virshup`
- :func:`~scanpy.tl.marker_gene_overlap` computes overlaps of marker genes :smaller:`thanks to M Luecken`
- :func:`~scanpy.tl.filter_rank_genes_groups` filters out genes based on fold change and fraction of cells expressing genes :smaller:`thanks to F Ramirez`
- :func:`~scanpy.pp.normalize_total` replaces :func:`~scanpy.pp.normalize_per_cell`, is more efficient and provides a parameter to only normalize using a fraction of expressed genes :smaller:`thanks to S Rybakov`
- :func:`~scanpy.pp.downsample_counts` has been sped up, changed default value of `replace` parameter to `False`, see :pr:`474` :smaller:`thanks to I Virshup`
- :func:`~scanpy.pl.embedding_density` allows plots of cell densities on embeddings, see :pr:`543` :smaller:`thanks to M Luecken`
- :func:`~scanpy.external.palantir` interfaces Palantir [Setty18]_, see :pr:`493` :smaller:`thanks to A Mousa`

Minor updates:
Code design:

- `.layers` support of scatter plots :smaller:`thanks to F Ramirez`
- fix double-logarithmization in compute of log fold change in :func:`~scanpy.tl.rank_genes_groups` :smaller:`thanks to A Muñoz-Rojas`
- fix return sections of docs :smaller:`thanks to P Angerer`
- :func:`~scanpy.pp.neighbors` and :func:`~scanpy.tl.umap` got rid of UMAP legacy code and introduced UMAP as a dependency :pr:`576` :noteversion:`1.4.2` :smaller:`thanks to S Rybakov`
- :func:`~scanpy.pp.calculate_qc_metrics` is single threaded by default for datasets under 300,000 cells -- allowing cached compilation :pr:`615` :noteversion:`1.4.3` :smaller:`thanks to I Virshup`
- `.layers` support of scatter plots :noteversion:`1.4.1` :smaller:`thanks to F Ramirez`
- fix double-logarithmization in compute of log fold change in :func:`~scanpy.tl.rank_genes_groups` :noteversion:`1.4.1` :smaller:`thanks to A Muñoz-Rojas`
- fix return sections of docs :noteversion:`1.4.1` :smaller:`thanks to P Angerer`


Version 1.4 :small:`February 5, 2019`
-------------------------------------

Major updates:

- one can now `import scanpy as sc` instead of `import scanpy.api as sc`, see :mod:`scanpy` :noteversion:`1.3.7`
- one can `import scanpy as sc` instead of `import scanpy.api as sc`, see :mod:`scanpy` :noteversion:`1.3.7`
- a new plotting gallery for :doc:`visualizing-marker-genes` :noteversion:`1.3.6` :smaller:`thanks to F Ramirez`
- tutorials are integrated on ReadTheDocs, :doc:`pbmc3k` and :doc:`paga-paul15` :noteversion:`1.3.6`
- a fully distributed preprocessing backend :noteversion:`1.3.3` :smaller:`thanks to T White and the Laserson Lab`
Expand Down Expand Up @@ -93,7 +80,7 @@ Plotting of marker genes and quality control, see this `section <https://scanpy.

- :func:`~scanpy.api.pl.dotplot` for visualizing genes across conditions and clusters, see `here <https://gist.github.com/fidelram/2289b7a8d6da055fb058ac9a79ed485c>`__ :smaller:`thanks to F Ramirez`
- :func:`~scanpy.api.pl.heatmap` for pretty heatmaps, see :pr:`175` :smaller:`thanks to F Ramirez`
- :func:`~scanpy.api.pl.violin` now produces very compact overview figures with many panels, see `here <https://github.com/theislab/scanpy/pull/175>`__ :smaller:`thanks to F Ramirez`
- :func:`~scanpy.api.pl.violin` produces very compact overview figures with many panels, see `here <https://github.com/theislab/scanpy/pull/175>`__ :smaller:`thanks to F Ramirez`
- :func:`~scanpy.api.pl.highest_expr_genes` for quality control, see :pr:`169`; plot genes with highest mean fraction of cells, similar to `plotQC` of *Scater* [McCarthy17]_ :smaller:`thanks to F Ramirez`

There is a `section <https://scanpy.readthedocs.io/en/latest/api/#imputation>`__ on imputation:
Expand All @@ -112,7 +99,7 @@ Version 1.1 :small:`May 31, 2018`
---------------------------------

- :func:`~scanpy.api.set_figure_params` by default passes `vector_friendly=True` and allows you to produce reasonablly sized pdfs by rasterizing large scatter plots
- :func:`~scanpy.api.tl.draw_graph` now defaults to the ForceAtlas2 layout [Jacomy14]_ [Chippada18]_, which is often more visually appealing and whose computation is much faster :smaller:`thanks to S Wollock`
- :func:`~scanpy.api.tl.draw_graph` defaults to the ForceAtlas2 layout [Jacomy14]_ [Chippada18]_, which is often more visually appealing and whose computation is much faster :smaller:`thanks to S Wollock`
- :func:`~scanpy.api.pl.scatter` also plots along variables axis :smaller:`thanks to MD Luecken`
- :func:`~scanpy.api.pp.pca` and :func:`~scanpy.api.pp.log1p` support chunk processing :smaller:`thanks to S Rybakov`
- :func:`~scanpy.api.pp.regress_out` is back to multiprocessing :smaller:`thanks to F Ramirez`
Expand Down Expand Up @@ -143,7 +130,7 @@ Upgrading to 1.0 isn't fully backwards compatible in the following changes:
- the graph-based tools :func:`~scanpy.api.tl.louvain`
:func:`~scanpy.api.tl.dpt` :func:`~scanpy.api.tl.draw_graph`
:func:`~scanpy.api.tl.umap` :func:`~scanpy.api.tl.diffmap`
:func:`~scanpy.api.tl.paga` now require prior computation of the graph:
:func:`~scanpy.api.tl.paga` require prior computation of the graph:
``sc.pp.neighbors(adata, n_neighbors=5); sc.tl.louvain(adata)`` instead of
previously ``sc.tl.louvain(adata, n_neighbors=5)``
- install `numba` via ``conda install numba``, which replaces cython
Expand All @@ -166,7 +153,7 @@ Further changes are:

- UMAP [McInnes18]_ can serve as a first visualization of the data just as tSNE,
in contrast to tSNE, UMAP directly embeds the single-cell graph and is faster;
UMAP is now also used for measuring connectivities and computing neighbors,
UMAP is also used for measuring connectivities and computing neighbors,
see :func:`~scanpy.api.pp.neighbors`
- graph abstraction: AGA is renamed to PAGA: :func:`~scanpy.api.tl.paga`; now,
it only measures connectivities between partitions of the single-cell graph,
Expand All @@ -175,18 +162,18 @@ Further changes are:
connectivity measure has been improved
- logistic regression for finding marker genes
:func:`~scanpy.api.tl.rank_genes_groups` with parameter `method='logreg'`
- :func:`~scanpy.api.tl.louvain` now provides a better implementation for
- :func:`~scanpy.api.tl.louvain` provides a better implementation for
reclustering via `restrict_to`
- scanpy no longer modifies rcParams upon import, call
`settings.set_figure_params` to set the 'scanpy style'
- default cache directory is ``./cache/``, set `settings.cachedir` to change
this; nested directories in this are now avoided
this; nested directories in this are avoided
- show edges in scatter plots based on graph visualization
:func:`~scanpy.api.tl.draw_graph` and :func:`~scanpy.api.umap` by passing
`edges=True`
- :func:`~scanpy.api.pp.downsample_counts` for downsampling counts :smaller:`thanks to MD Luecken`
- default 'louvain_groups' are now called 'louvain'
- 'X_diffmap' now contains the zero component, plotting remains unchanged
- default 'louvain_groups' are called 'louvain'
- 'X_diffmap' contains the zero component, plotting remains unchanged


Version 0.4.4 :small:`February 26, 2018`
Expand Down Expand Up @@ -243,7 +230,7 @@ Initial release of `partition-based graph abstraction (PAGA) <https://github.com
Version 0.2.1 :small:`July 24, 2017`
---------------------------------------

Scanpy now includes preprocessing, visualization, clustering, pseudotime and
Scanpy includes preprocessing, visualization, clustering, pseudotime and
trajectory inference, differential expression testing and simulation of gene
regulatory networks. The implementation efficiently deals with datasets of more
than one million cells.
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