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BarPlots also with simulated data #210

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MerktSimon opened this issue Jan 11, 2020 · 4 comments
Closed

BarPlots also with simulated data #210

MerktSimon opened this issue Jan 11, 2020 · 4 comments
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enhancement New feature or request visualization

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@MerktSimon
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@MerktSimon MerktSimon added enhancement New feature or request visualization labels Jan 11, 2020
@MerktSimon MerktSimon self-assigned this Jan 11, 2020
@MerktSimon
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any opinions on color coding?
Measurement, Simulation pairs could have same color but e.g. simulation with stripes or all measurements could have the same color and simulation an other.

@yannikschaelte
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both would make sense I think. depends on how many data, how many conditions etc. having measurement one color, simulation the other would allow to directly see if both match overall. but for that aim also stripes and no stripes would suffice. (assuming the sim-meas pairs are always plotted in direct neighborhood). in addition, one could however also want to have separate colors for different conditions / data groups.

MerktSimon added a commit that referenced this issue Jan 15, 2020
@MerktSimon
resolves #210
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so we could make this an option or just fix a number like 5 and say: up to this number there will be different colors and above we will only differ between measurement and simulation.

@MerktSimon MerktSimon mentioned this issue Jan 15, 2020
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it is now implemented for now with same color for each measurement/simulation pair

@MerktSimon MerktSimon reopened this Jan 24, 2020
LeonardSchmiester added a commit that referenced this issue Feb 11, 2020
@PhilippStaedter @dweindl
@yannikschaelte @LeonardSchmiester @MerktSimon @plakrisenko @LaraFuhrmann
Develop (#284)
efe91cc 
* Add pylint config

* Fixes ys (#237)

* fix merge error

* add petablint yaml test

* add parameters test

* Parameter mapping should include all model parameters (#235)

Closes #103

* Parameter mapping should include all model parameters
* Known values should be filled in
* Extend and update tests
* Refactor parameter mapping
* properly handle estimated and non-estimated parameters
* Fix wrong parameter scale returned from mapping
* ...

* Allow initial concentrations / sizes in condition table (#238)

* Allow species and compartments in condition table

* Updated doc allowing for states etc in condition file

* Update pylint: allow lower-case constants

* Export __format_version__

* Fix returning floats as strings in case there are parameter names in the condition table

Co-authored-by: LeonardSchmiester <leonard.schmiester@helmholtz-muenchen.de>

* Barplots and Replicates with Simulation data (#214)

Fixes #196, fixes #210, fixes #213

* Cleanup visualization (#240)

* Add constants for visualization field IDs
* .. and some others
* start using them
* formatting, ...

* Observables table instead of SBML assignment rules (#244)

Closes #201, closes #241 

* Update data format doc for observable table

* Add field name constants for observable table

* Add observables table to petab.Problem

* Update YAML schema and CompositeProblem

* Add functions for writing PEtab dataframes to files

* Deprecate SBML-observable functions

* Implement validation for observable table

* Add function for converting SBML-observable models to observable table

* Use costants for PEtab table fields

* Update PEtab files illustration

* Fix most pylint issues (Closes #234)

* Update vis to observalble table (Closes #246)

  No need to check for equal NOISE_DISTRIBUTION and OBSERVABLE_TRANSFORMATION anymore, so they are no longer included in the measurement table, and cannot differ for the same observableId

* Fix and update flatten_timepoint_specific_output_overrides

  Closes #247

  Was creating wrong observables before

* Address review comments

  Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com>

* Release 0.1.0; file format version 1

* Fix parameter mapping: include output parameters not present in SBML model

* Add convenience functions to petab.Problem

* get_optimization_parameter_scales
* get_optimization_to_simulation_scale_mapping
* add tests

* Fix petab/petab_schema.yaml missing in pypi package

* Update pylint ignorelist

* Update README

* Remove obsolete functions

... related to hierarchical optimization, which should be kept outside PEtab

* Let get_placeholders return an (ordered) list of placeholders

because it is much more useful

* Add check for valid identifiers (Closes #179) (#253)

Co-authored-by: Polina Lakrisenko <p.lakrisenko@gmail.com>

* Deprecate petab.problem.from_folder (Closes #245)

... as well as get_default_*_file_name

* Release 0.1.1

* Barplot uniform coloring & yScale=log fix #196 (#255)


* resolves #197

* small fix

* change all barplot colors to blue

* allow to extract only estimate parameters (#256)

* allow to extract only estimate parameters

* add docstrings

* Visu callobs par (#262)

* fix #261

* corrected flake8 error - line too long

* deleted white space

* add F403 to falke8 tests

* Fix handling of numeric observable/noiseFormula in observable table (Fixes #264)

* Add properties for fixed/free and scaled values (#268)

* allow to extract only estimate parameters

* add docstrings

* return scaled versions of arrays

* Update petab/problem.py

Co-Authored-By: Daniel Weindl <dweindl@users.noreply.github.com>

Co-authored-by: Daniel Weindl <dweindl@users.noreply.github.com>

* Observables function (#269)

* allow to extract only estimate parameters

* add docstrings

* return scaled versions of arrays

* Update petab/problem.py

Co-Authored-By: Daniel Weindl <dweindl@users.noreply.github.com>

* add get_observables function

* add observables test; use observables file in petab test

* fix typo

* move get_observables to ..._ids

* remove unused arg

* add docstring

* fix lint

* fix pylint

* fix flake8

Co-authored-by: Daniel Weindl <dweindl@users.noreply.github.com>

* Fix documentation hierarchy

* Add functions to get all of fixed|free, scaled parameter values (#273)

* allow to extract only estimate parameters

* add docstrings

* return scaled versions of arrays

* Update petab/problem.py

Co-Authored-By: Daniel Weindl <dweindl@users.noreply.github.com>

* add get_observables function

* add observables test; use observables file in petab test

* fix typo

* move get_observables to ..._ids

* remove unused arg

* add docstring

* fix lint

* fix pylint

* fix flake8

* fix typo

* streamline fixed|free|all, and scaled values

* fix default args

* fix codacy

* address reviewer comment: return empty list

* add docstring#

* add more docstrings

* fix var type error

* address reviewer comments

Co-authored-by: Daniel Weindl <dweindl@users.noreply.github.com>

* Default column to look for simulation results should be 'simulation'

* PEtab COMBINE archives (#271)

* Add create_combine_archive for generation of COMBINE archives

* Add support for reading PEtab COMBINE archives

* Add tests for COMBINE archive r/w

* Fix sbml_observables_to_table - got broken in eb5453

* Increase test coverage (#278)

* allow to extract only estimate parameters

* add docstrings

* return scaled versions of arrays

* Update petab/problem.py

Co-Authored-By: Daniel Weindl <dweindl@users.noreply.github.com>

* add get_observables function

* add observables test; use observables file in petab test

* fix typo

* move get_observables to ..._ids

* remove unused arg

* add docstring

* fix lint

* fix pylint

* fix flake8

* fix typo

* streamline fixed|free|all, and scaled values

* fix default args

* fix codacy

* address reviewer comment: return empty list

* add docstring#

* add more docstrings

* fix var type error

* address reviewer comments

* add parameter properties test

* add tests for get/write_parameter_df

* add measurements tests

* add conditions tests

* fix conditions create function

* add parameter tests

* add observables tests

* fixup

* add docstrings

* address reviewer comments

* random edit to see if codacy is happy

* random stuff to annoy codecov

Co-authored-by: Daniel Weindl <dweindl@users.noreply.github.com>

Co-authored-by: Daniel Weindl <dweindl@users.noreply.github.com>
Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com>
Co-authored-by: LeonardSchmiester <leonard.schmiester@helmholtz-muenchen.de>
Co-authored-by: Simon Merkt <49190262+MerktSimon@users.noreply.github.com>
Co-authored-by: Polina Lakrisenko <p.lakrisenko@gmail.com>
Co-authored-by: LaraFuhrmann <55209716+LaraFuhrmann@users.noreply.github.com>
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