Release Notes¶
Version 0.2.5 Oct 14, 2022¶
Changes:
Catch non-positive parameter values and raise a ValueError if necessary (PR 614).
get_mean_var uses the same size parameter for mean and variance (PR 698).
Bugfixes:
filter_genes now works with adata.layers[‘unspliced’] being sparse and adata.layers[‘spliced’] dense (PR 537).
show_proportions actually considers the layer “ambiguous” if present (PR 587).
Fix calculation of Pearson’s correlation in csr_vcorrcoef (PR 679).
Fix get_mean_var to work with sparse input and ignore_zeros=True (PR 698).
Fix bug in neighbor calculation (PR 797).
Fix optimization.py::get_weight to work with numeric, non-integer values (PR 839).
Fix inference with fit_scaling=False (PR 848).
Fix saving of velocity embedding stream (PR 900).
Fix Pandas’ display precison when passed to get_df (PR 907).
Version 0.2.4 Aug 26, 2021¶
Perspectives:
Landing page and two notebooks accompanying the perspectives manuscript at MSB.
New datasets: Gastrulation, bone marrow, and PBMCs.
New capabilities:
Added vignettes accompanying the NBT manuscript.
Kinetic simulations with time-dependent rates.
New arguments for tl.velocity_embedding_stream (PR 492).
Introduced automated code formatting flake8 and isort (PR 360, PR 374).
tl.velocity_graph parallelized (PR 392).
legend_align_text parameter in pl.scatter for smart placing of labels without overlapping.
Save option for pl.proportions.
Bugfixes:
Pinned sphinx<4.0 and nbsphinx<0.8.7.
Fix IPython import at CLI.
Version 0.2.3 Feb 13, 2021¶
tl.recover_dynamics: Multicore implementation thanks to M Klein, Y Schaelte, P Weiler
CI now runs on GitHub Actions
New utility functions:
utils.gene_info: Retrieve gene information from biothings client.
utils.convert_to_ensembl and utils.convert_to_gene_names: Converting ensembl IDs into gene names and vice versa.
Version 0.2.2 July 22, 2020¶
tl.paga: PAGA graph with velocity-directed edges.
Black code style
Version 0.2.1 May 28, 2020¶
Bugfixes:
Correct identification of root cells in tl.latent_time thanks to M Lange
Correct usage of latent_time prior in tl.paga thanks to G Lubatti
Version 0.2.0 May 12, 2020¶
New vignettes:
RNA velocity basics
Dynamical Modeling
Differential Kinetics
Tools:
tl.differential_kinetic_test: introduced a statistical test to detect different kinetic regimes.
tl.rank_dynamical_genes: introduced a gene ranking by cluster-wise likelihoods.
tl.paga: introduced directed PAGA graph
Plotting:
pl.scatter enhancements: linear and polynomical fits, gradient coloring
pl.proportions: Pie and bar chart of spliced/unspliced proprtions.
GridSpec: multiplot environment.
Version 0.1.20 Sep 5, 2019¶
Tools:
tl.recover_dynamics: introduced a dynamical model inferring the full splicing kinetics, thereby identifying all kinetic rates of transcription, splicing and degradation.
tl.recover_latent_time: infers a shared latent time across all genes based on the learned splicing dynamics.
Plotting:
pl.scatter enhancements: multiplots, rugplot, linear and polynomial fits, density plots, etc.
pl.heatmap: heatmap / clustermap of genes along time coordinate sorted by expression along dynamics.
Preprocessing:
New attributes in pp.filter_genes: min_shared_counts and min_shared_genes.
Added fast neighbor search method: Hierarchical Navigable Small World graphs (HNSW)
Version 0.1.14 Dec 7, 2018¶
Plotting:
New attriutes arrow_length and arrow_size for flexible adjustment of embedded velocities.
pl.velocity_graph: Scatter plot of embedding with cell-to-cell transition connectivities.
pl.velocity_embedding_stream: Streamplot visualization of velocities.
Improve visualization of embedded single cell velocities (autosize, colors etc.)
Tools:
tl.cell_fate: compute cell-specific terminal state likelihood
New attribute approx=True in tl.velocity_graph to enable approximate graph computation by performing cosine correlations on PCA space.
Preprocessing:
Automatically detect whether data is already preprocessed.
Version 0.1.11 Oct 27, 2018¶
Plotting:
settings.set_figure_params(): adjust matplotlib defaults for beautified plots
improved default point and arrow sizes; improved quiver autoscale
enable direct plotting of
Tools:
tl.velocity_confidence: Added two confidence measures ‘velocity_confidence’ and ‘velocity_confidence_transition’.
tl.rank_velocity_genes: Added functionality to rank genes for velocity characterizing groups using a t-test.
New attribute perc in tl.velocity enables extreme quantile fit, e.g. set perc=95.
New attribute groups in tl.velocity enables velocity estimation only on a subset of the data.
Improved tl.transition_matrix by incorporating self-loops via self_transitions=True and state changes that have negative correlation with velocity (opposite direction) via use_negative_cosines=True
Utils:
utils.merge to merge to AnnData objects such as already existing AnnData and newly generated Loom File.
Version 0.1.8 Sep 12, 2018¶
Plotting:
support saving plots as pdf, png etc.
support multiple colors and layers
quiver autoscaling for velocity plots
attributes added: figsize and dpi
Preprocessing:
filter_and_normalize() instead of recipe_velocity()
normalization of layers is done automatically when computing moments
Tools:
terminal_states: computes root and end points via eigenvalue decomposition thanks to M Lange
Version 0.1.5 Sep 4, 2018¶
Support writing loom files
Support both dense and sparse layers
Plotting bugfixes
Added pp.recipe_velocity()
Version 0.1.2 Aug 21, 2018¶
First alpha release of scvelo.