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feat(plots): plot inferred time-clonal fate potency correlation #647

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feat(plots): plot inferred time-clonal fate potency correlation #647

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Commits on Aug 23, 2024

  1. fix(plots): use vector field basis in shared time uncertainty plot 

    Signed-off-by: Cameron Smith <[email protected]>
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  2. fix(utils): add array-based type class aliases 

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  3. fix(utils): remove unused comments 

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  4. feat(utils): include size and category information in data string rep… 

    …resentation

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Commits on Aug 24, 2024

  1. feat(plots): draft lineage fate correlation plot 

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  2. refactor(plots): rename vector field uncertainty plot function 

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  3. fix(plots): enable type-checking of plot lineage fate correlation 

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  4. fix(plots): export lineage fate correlation plot from plots package 

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  5. fix(io): serialize np.bool_ to bool 

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  6. refactor(tasks): migrate data subset functionality to io package 

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  7. refactor(tasks): move load data function to utils 

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Commits on Aug 25, 2024

  1. feat(utils): add function to compute file hashes 

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  2. fix(plots): type-check get clone trajectory function 

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  3. fix(plots): use pandas regex str replacement in lineage fate correlation 

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  4. refactor(plots): archive unused code from get clone trajectory 

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  5. feat(styles): add module for explicit specification of colors 

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  6. fix(plots): parameterize posterior time color map 

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  7. nit(plots): update comments 

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  8. fix(plots): include time and angle uncertainty 

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  9. feat(tasks): draft time fate correlation task 

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  10. fix(plots): disable transparency in lineage fate correlation 

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Commits on Aug 26, 2024

  1. feat(workflows): add demo flag 

    automatically set all flags to demo mode

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  2. fix(plots): make posterior time titles and colorbar optional 

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  3. fix(plots): reorder angle uncertainty of lineage fate correlation 

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  4. fix(tasks): map time fate correlation over all data set configurations 

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  5. fix(plots): allow scaled measures as well as vector fields 

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  6. fix(styles): enable unicode in latex 

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  7. feat(styles): add function to set matplotlib style globally 

    - check if latex is in path
- TODO: the latex distribution requires standard packages that may only be able to be checked via tlmgr

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  8. fix(plots): update lineage fate correlation titles and font size 

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  9. fix(tasks): update time lineage fate correlation layout parameters 

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Commits on Aug 27, 2024

  1. fix(bazel): add mplstyle as data 

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  2. fix(summarize): use constant cell type colors 

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  3. fix(plots): accept List[Axes] input type 

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  4. fix(plots): add legend data to cell type plot 

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  5. fix(tasks): add row labels and external legend 

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  6. fix(plots): update vector field summary interface 

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  7. fix(tasks): update time lineage fate correlation legend spacing 

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  8. fix(plots): reduce likelihood of mutation by copying mutated input 

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  9. fix(plots): automatically increment axis indices in lineage fate corr… 

    …elation

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  10. fix(plots): parameterize transparency of posterior time 

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  11. fix(tasks): include column-level colorbars in gridspec 

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  12. deps(pyproject): add ipdb to test group 

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  13. chore(bazel): sync lock 

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Commits on Aug 28, 2024

  1. fix(plots): remove redundant data input from lineage fate correlation 

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  2. fix(tasks): refactor time fate correlation and note redundancy with w… 

    …orkflow task

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  3. fix(workflows): add posterior samples and postprocessed data to summa… 

    …rize outputs class

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  4. feat(workflows): add task to generate time lineage fate correlation a… 

    …nalysis

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  5. chore(workflows): bump summarize cache to 2024.8.15.1 

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  6. feat(io): add function to generate and save separate and combined met… 

    …rics tables

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  7. fix(workflows): include png in time lineage fate correlation plot upl… 

    …oads

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  8. fix(workflows): include individual metric tables in CombinedMetricsOu… 

    …tputs

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  9. fix(workflows): use helper function to generate and save metrics tables 

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  10. refactor(io): rename json module to metrics 

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  11. fix(io): default to sans serif in table tex wrapper 

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  12. feat(plots): add functions to render graphical model sketches 

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  13. fix(workflows): io.json -> io.metrics 

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Commits on Aug 29, 2024

  1. feat(io): log dataset hash on load 

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  2. fix(utils): log data hash on load 

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  3. refactor(utils): move hash function to io 

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  4. refactor(datasets): update hash file import 

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  5. fix(io): log data hash on pickle save/load 

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  6. refactor(utils): move hash file tests to separate module 

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  7. fix(styles): remove unused mplstyle key 

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  8. fix(plots): filter invalid adjustText warning 

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  9. fix(tasks): set 4 columns for time fate correlation legend 

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  10. fix(plots): update vector field summary plot 

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  11. fix(plots): filter invalid adjustText warning if logger is available 

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Commits on Aug 30, 2024

  1. test(plots): add modular layout function 

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  2. fix(io): use dill to support pickling matplotlib objects 

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  3. test(scripts): add h5 scripts 

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  4. fix(deps): explicitly lower bound dill 

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  5. feat(plots): serialize figure layout and its panels separately 

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  6. fix(plots): show mean and CV histograms in shared time uncertainty 

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Commits on Aug 31, 2024

  1. fix(plots): use gridspec for shared time uncertainty plot 

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  2. fix(plots): default to CV in vector field plot 

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  3. fix(io): change sparsification notice from warning to debug level 

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  4. feat(plots): set base for report 

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Commits on Sep 1, 2024

  1. fix(models): include std of predictive samples in posterior dict 

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  2. fix(plots): allow setting axis-level label for colorbars 

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  3. fix(analysis): remove unused list wrappers 

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Commits on Sep 3, 2024

  1. feat(plots): support SubplotSpec for plot_gene_ranking 

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  2. feat(plots): support SubplotSpec for plot_parameter_posteriors 

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  3. feat(plots): support SubplotSpec for plot_vector_field_summary 

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Commits on Sep 4, 2024

  1. fix(plots): use pure text title for plot gene ranking 

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  2. fix(plots): update major log tick labels for parameter posteriors 

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    cameronraysmith committed Sep 4, 2024
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  3. fix(plots): force min-max colorbar tick labels for bounded variables 

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  4. feat(plots): support SubplotSpec for rainbowplot 

    - temporarily use independent function `rainbowplot_module` for testing purposes

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  5. refactor(plots): extract report subgrid plots 

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Commits on Sep 5, 2024

  1. fix(plots): parametrize rainbow plot default fontsize 

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  2. fix(plots): organize reporting function for use in summarization task 

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  3. fix(tasks): reorganize summarize in preparation for integration of re… 

    …porting module

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Commits on Sep 6, 2024

  1. feat(workflows): add selected genes configuration to data sets 

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  2. fix(plots): move reporting function imports to docstring 

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  3. refactor(plots): import reporting functions through plots package 

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  4. fix(tasks): import reporting functions in summarize task 

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  5. refactor(plots): rename selected genes variable 

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  6. refactor(plots): rename selected genes variable in report 

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  7. fix(plots): disable text axes in self-generated figure 

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  8. nit(plots): reorder report arguments and produce png output 

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  9. fix(tasks): use report instead of plot gene summary 

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  10. fix(workflows): use correct WorkflowConfiguration field name 

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  11. fix(workflows): use SummarizeConfiguration to access selected genes 

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  12. chore(workflows): bump postprocess cache 2024.8.15.1 

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  13. fix(plots): unpack width ratios in rainbow plot 

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  14. fix(plots): parameterize state color dictionary 

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  15. fix(tasks): use parameterized state color dictionary 

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  16. fix(workflows): reset configurations 

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  17. fix(models): retain gene ranking data for all genes 

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  18. chore(workflows): bump postprocess cache 2024.8.15.2 

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  19. feat(io): check and log error for mismatching data download hashes 

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  20. fix(analysis): add max genes per bin argument to top_mae_genes 

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  21. fix(tasks): set top mae genes max genes per bin to 5 

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  22. fix(workflows): upload figure object files 

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  23. fix(plots): use black box plots 

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  24. fix(analysis): parameterize top mae genes gene filter 

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  25. fix(plots): retain order of selected genes in report 

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  26. fix(tasks): update vector field summary parameters 

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  27. feat(io): check data download hashes before and after download prepro… 

    …cessing

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Commits on Sep 7, 2024

  1. fix(plots): default parameter posteriors to box plot 

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  2. fix(plots): disable default box plot 

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  3. feat(utils): add function to compute the quartile coefficient of disp… 

    …ersion

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  4. fix(plots): use quartile coefficient of dispersion to quantify tempor… 

    …al uncertainty

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  5. fix(report): update docstring 

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  6. fix(plots): update report dpi 

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  7. fix(plots): set vector field uncertainty default plot type to hexbin 

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  8. fix(plots): set posterior time default plot type to hexbin 

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  9. fix(tasks): set min mae percentile from candidate dataframe length 

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  10. fix(plots): increase box plot width 

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  11. fix(plots): add parameter to truncate high error genes by percentile 

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  12. fix(plots): set rainbow default plot type to hexbin 

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Commits on Sep 9, 2024

  1. chore(workflows): bump summarize cache to 2024.8.15.3 

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Commits on Sep 10, 2024

  1. nit(models): default to kwargs 

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Commits on Sep 12, 2024

  1. test(models): exercise guide_type and add_offset parameters of the Ve… 

    …locityModel class

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Commits on Sep 13, 2024

  1. test(models): remove unused model parameters 

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  2. refactor(models): remove unused parameters from velocity_model 

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  3. Revert "refactor(models): remove unused parameters from velocity_model" 

    This reverts commit b18e120.
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  4. Revert "test(models): remove unused model parameters" 

    This reverts commit 50d4970.
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  5. fix(models): mark apparently unused sample sites 

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  6. fix(plots): include median in parameter plots 

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  7. refactor(plots): move setup_colors to utils 

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  8. fix(plots): use QCD instead of CV in shared time histogram 

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  9. fix(plots): synchronize vector field color map with rainbowplots 

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  10. fix(plots): pass boxplot flag to parameter posteriors 

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Commits on Sep 14, 2024

  1. feat(plots): use mae percentile in gene ranking plot 

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  2. fix(analysis): update compute volcano data interface types 

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Commits on Sep 15, 2024

  1. fix(utils): include type in dictionary log 

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Commits on Sep 16, 2024

  1. fix(plots): make mae scale default for gene ranking 

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  2. fix(plots): remove unused comment from posterior predictive extrapola… 

    …tion

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  3. fix(plots): remove additional unused comments from posterior predicti… 

    …ve extrapolation

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Commits on Sep 17, 2024

  1. fix(analysis): update mae_per_gene function and add docstring 

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  2. fix(analysis): remove unused comments from compute_volcano_data 

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  3. fix(plots): optionally force recomputation of volcano data 

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  4. fix(plots): parameterize inclusion of complete angular scale 

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  5. fix(analysis): add shadow support for jax arrays 

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  6. test(analysis): add basic tests for mae_per_gene 

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  7. feat(tests): add function to generate fixture data 

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  8. feat(tests): test ability to load and log data string diff with seria… 

    …lized

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  9. fix(tests): add serialization test for uns dict with nested numpy array 

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  10. feat(tests): add preprocessed pancreas 50x13 fixture data 

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  11. fix(io): add debug logging of attempted serialization dictionary to s… 

    …erialize anndata

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Commits on Sep 18, 2024

  1. fix(tasks): add soft support for selected genes to preprocessing 

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  2. fix(io): restore types when deserializing json 

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  3. fix(tests): note handling of selected genes in generate fixture data 

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  4. fix(tests): add unprocessed data fixture 

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  5. fix(tests): add processed data fixture 

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  6. wip(tests): sketch smoke test execution of VelocityModule 

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  7. fix(tests): rename small deserialized data fixture in plots 

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  8. fix(tests): load preprocessed deserialized data fixture globally 

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  9. fix(interfaces): add default factory for preprocess selected_genes em… 

    …pty list

resolves

```
ValueError: mutable default <class 'list'> for field selected_genes is not allowed: use default_factory
```

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  10. feat(io): optionally check file hashes when (de)serializing json files 

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  11. test(io): update serialization tests with expectation specs 

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    cameronraysmith committed Sep 18, 2024
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  12. fix(tests): update fixture name for preprocessed_3_4 in plot histograms 

    Signed-off-by: Cameron Smith <[email protected]>
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    cameronraysmith committed Sep 18, 2024
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  13. fix(tests): exercise hash check in data serialization 

    Signed-off-by: Cameron Smith <[email protected]>
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    cameronraysmith committed Sep 18, 2024
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  14. feat(tests): add function to generate postprocessed fixture data 

    Signed-off-by: Cameron Smith <[email protected]>
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    cameronraysmith committed Sep 18, 2024
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  15. test(train): add unit test for train task on static fixture data 

    Signed-off-by: Cameron Smith <[email protected]>
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    cameronraysmith committed Sep 18, 2024
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  16. tests(data): add trained pancreas 50 by 7 fixture 

    Signed-off-by: Cameron Smith <[email protected]>
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    cameronraysmith committed Sep 18, 2024
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  17. tests(data): add postprocessed pancreas 50 by 7 fixture 

    Signed-off-by: Cameron Smith <[email protected]>
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    cameronraysmith committed Sep 18, 2024
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