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Make esqlabsR theme for default plot configuration #225

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PavelBal opened this issue May 11, 2022 · 6 comments · Fixed by #265
Closed

Make esqlabsR theme for default plot configuration #225

PavelBal opened this issue May 11, 2022 · 6 comments · Fixed by #265
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@IndrajeetPatil

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@PavelBal
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Including sim results mapping to both color and line types. Should be loaded automatically when loading the package.
@IndrajeetPatil
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It will be a class, not a theme.

esqLABS members will need to create an instance of this class and pass it as argument to the respective parameter in the plotting functions.

@PavelBal
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Wait, I though this is exactly why we have different themes - to specify such defaults? From Michaels comment I think he understands it the same way Open-Systems-Pharmacology/OSPSuite-R#871 (comment)

@IndrajeetPatil
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We don't have a theme parameter anymore (cf. Open-Systems-Pharmacology/OSPSuite-R#833 (comment)). We only take a plot configuration object.

@PavelBal
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But I thought that the default plot configuration is created based on the theme.

@IndrajeetPatil
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Nope, theme is not being used anywhere.

We had considered the possibility of introducing a new function that can convert an existing theme to a plot configuration object.

@PavelBal
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As we probably would like to have some default values that differ from the defaults in ospsuite, creating a DefaultPlotConfiguration from the package's theme become impotant. This feature should be implemented.

IndrajeetPatil added a commit that referenced this issue Jun 8, 2022
@IndrajeetPatil
Add functions to create plotting-related configs
797825c 
- [x] Closes #262
- [x] Closes #263
- [x] Closes #264
- [x] Closes #225
- [x] docs and NEWS
- [x] tests
@IndrajeetPatil IndrajeetPatil mentioned this issue Jun 8, 2022
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IndrajeetPatil added a commit that referenced this issue Jun 8, 2022
@IndrajeetPatil
Add functions to create plotting-related configs (#265)
9692458 
- [x] Closes #262
- [x] Closes #263
- [x] Closes #264
- [x] Closes #225
- [x] docs and NEWS
- [x] tests
PavelBal added a commit that referenced this issue Sep 26, 2022
@PavelBal @IndrajeetPatil
@hannaei @svavil
Dev to main for Release V4. (#328)
a372dfb 
* Create V4  (#255)

* - Update data-handling vignette
- Function `loadObservedData()` requires a `ProjectConfiguration` instead of a
`ScenarioConfiguration`.

* Remove unused vignettes

* Update AppVeyor to R4.2.0

* Increment version to v4.0.0

* Cleanup for v4

* Update website

* Update reference index

* Removed steady-state function and using ospsuite.parameteridentification (#261)

* Removed steady-state function and using ospsuite.parameteridentification

* Update NEWS.md

Co-authored-by: Indrajeet Patil <[email protected]>

* Removed unused message

* Update documentation

* Update appveyor.yml

* Fix examples

Co-authored-by: Indrajeet Patil <[email protected]>

* Add functions to create plotting-related configs (#265)

- [x] Closes #262
- [x] Closes #263
- [x] Closes #264
- [x] Closes #225
- [x] docs and NEWS
- [x] tests

* Following guidelines for internal function names (#266)

* Added simulationRunOptions parameter (#268)

* Added simulationRunOptions parameter

* Remove `hash` from imports
Adds `stringr` and `labeling` to imports
Remove "return" from an empty switch statement
Missing documented arguments

* Update to roxygen2 7.2.1 (#273)

* Update to roxygen2 7.2.1

* .rd files

* Update exportSteadyStateToXLS.Rd

* Don't write to sheets when there is no data (#274)

Closes #272

* SensitivityAnalysis - use "by path" methods (#271)

* Use unlist

* Assign condition to a variable

* Skipping tests that rely on PK-Sim

* fix `createEsqlabsPlotConfiguration()`

Co-authored-by: Indrajeet Patil <[email protected]>

* Follow coding convention for source code filenames (#275)

* remove empty section from reference page

* Fix failing sensitivity-calculation after ospsuite update (#278)

* Fix failing sensitivity-calculation after ospsuite update

* Update rd

* Add tests for utilities (#280)

* Add tests for file utilities

* snapshot paths have changed?

* skip for now

* try

* problematic test?

* Update test-utilities-file.R

* Update test-utilities-file.R

* Update test-utilities-file.R

* Test for `compareWithNA()`

* rudimentary test for `ScenarioConfiguration`

* Don't skip tests on CI anymore (#283)

* Update README (#282)

* Update README

Closes #281

* Update README.md

* Tests for color utilities and global settings (#285)

* Tests for color utilities

* tests for global settings

* Use functions for error messages

* Additional tests for utilities (#287)

* Additional tests for utilities

* test for `compareSimulationParameters()`

* tweak tests for settings

* Test for `sampleRandomValue()`

* Address review comments

* remove `expect_s3_class()` for R6

* Extract applications (#288)

* - Add a function `getAllApplicationParameters` that returns all parameters of applications in a simulation
- Add a function `exportParametersToXLS` to write parameter information into an excel file that can be loaded in MoBi or R
- Add a function `writeExcel` that is a wrapper for creating a directory (if not present) and writing to excel file

* Update documentation

* Update R/utilities-simulation.R

Co-authored-by: Indrajeet Patil <[email protected]>

* Update R/utilities-parameters.R

Co-authored-by: Indrajeet Patil <[email protected]>

* Address review comments

* Update required R version

* Update NEWS

Co-authored-by: Indrajeet Patil <[email protected]>

* Tests for shiny apps (#290)

* Get rid of a few lints (#291)

* also not used

* - Add default project configuration file (#293)

- Fix documentation for the simulationTime argument of ScenarioConfiguration
- Fix example for setParameterValuesByPathWithCondition
- If simulation time is not defined in the ScenarioConfiguration, use output time schema from the simulation

* More tests for utilities (#294)

* More tests for utilities

* use github version

* skip for now

* Test for `executeInParallel()`

* Try shipping binary

* Revert "Try shipping binary"

This reverts commit 72dda5d.

* Update documentation (#298)

* More tests for scenario config (#296)

* more tests for scenario config

* to shut up codecov

* Get rid of `.getNetHashCode()`

Closes #297

* Added example project

* Add logo for the package (#299)

Stickers are big in the R community, and a good way to market ourselves at conferences and meetings. Print them, and distribute them, so that people can put them on their laptops.

cc @StephanSchaller

* - Remove unused test files
- Styler

* Delete modeling_environment.R

unneeded for the esqlabsR purposes

* Documenting data handling and running simulations (#301)

* Updated the introduction part of the vignette

* Data handling vignette

* Vignette on running simulations

* Propagated vignette updates to the /docs folder

* Updated links to the scenario file to avoid duplicated files

* style

* style changes to vignettes/data-handling.Rmd

Co-authored-by: Indrajeet Patil <[email protected]>

* Restored _snaps files that were mistakenly removed

* wording in introduction

Co-authored-by: Pavel Balazki <[email protected]>

* link to aciclovir model

Co-authored-by: Pavel Balazki <[email protected]>

* Removed function reference, moved installation and contribution to README.md only

* style changes README.md

Co-authored-by: Indrajeet Patil <[email protected]>

* Removed auto-generated testthat file

* Update vignettes/introduction-esqlabsr.Rmd

* Changes to data-handling.Rmd

Co-authored-by: Indrajeet Patil <[email protected]>
Co-authored-by: Pavel Balazki <[email protected]>

* Better explanation of the configuration Excel files

* Restructuring of existing documentation, a clear description of no-code approach

* Run tests for Shiny apps (#303)

* Simulations vignette with references to all configuration files and first lines of output

* Fixed link to the Scenarios.xlsx file

* Visualization vignette

* Sensitivity vignette

* Add getMoleculeNameFromQuantity() (#307)

* Add getMoleculeNameFromQuantity()

* Apply suggestions from code review

Co-authored-by: Indrajeet Patil <[email protected]>

Co-authored-by: Indrajeet Patil <[email protected]>

* Changed plot sizes

* Added troubleshooting sections

* Apply suggestions from code review

style changes

Co-authored-by: Indrajeet Patil <[email protected]>

* Apply suggestions from code review

style changes

Co-authored-by: Indrajeet Patil <[email protected]>

* Renamed chunks to follow style guide

* Added time profiles to sensitivity analysis

* Update vignettes/sensitivity-analysis.Rmd

* Added link to time profiles

* Updated the HTML docs to match the RMD docs (#309)

* Updated the HTML docs to match the RMD docs

* correct typos

Co-authored-by: Indrajeet Patil <[email protected]>

* Suggestions for vignettes (#315)

Co-authored-by: Johanna Eitel <[email protected]>

* Fixes initializeSimulation() when additionalParams is empty but not NULL #313 (#314)

* Added script for installation

* - List for packages that will be installed from CRAN
- Add "purr" explicitly to be installed from CRAN

* - Add jsonlite to be installed

* - Change defaults for `updatePackages` argument to `FALSE`
- Change defaults for `developerVersion` to `TRUE`
- Remove redundant test for PK-Sim connection

* Add vignette for shiny apps (#316)

* Add vignette for shiny apps

* Added header, minor style changes

* Add ShinyApp link to the introduction
Some minor changes to the vignette

Co-authored-by: Johanna Eitel <[email protected]>
Co-authored-by: Sergei Vavilov <[email protected]>
Co-authored-by: Pavel Balazki <[email protected]>

* Update website (#327)

* - Remove RData
- Update readme

* Update docs

Co-authored-by: Indrajeet Patil <[email protected]>
Co-authored-by: Johanna Eitel <[email protected]>
Co-authored-by: Sergei Vavilov <[email protected]>
Co-authored-by: Johanna Eitel <[email protected]>
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Add functions to create plotting-related configs esqLABS/esqlabsR
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@IndrajeetPatil @PavelBal