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Add plot configuration class and time profile plots #871

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May 11, 2022
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37e2197
adds first drafts for plot config function + class
IndrajeetPatil Apr 4, 2022
8de281b
more aesthetics
IndrajeetPatil Apr 4, 2022
4461041
cover more properties
IndrajeetPatil Apr 4, 2022
ad233e4
remaining not necessary, or derivative of existing
IndrajeetPatil Apr 4, 2022
5a3799a
docs
IndrajeetPatil Apr 4, 2022
447925b
Merge branch 'develop' into 833_create_plot_configuration
IndrajeetPatil Apr 5, 2022
2909f7c
docs
IndrajeetPatil Apr 5, 2022
cff38fd
fixes
IndrajeetPatil Apr 5, 2022
fffa94d
Merge branch 'develop' into 833_create_plot_configuration
IndrajeetPatil Apr 5, 2022
7ad6df6
Merge branch 'develop' into 833_create_plot_configuration
IndrajeetPatil Apr 5, 2022
77d070c
remove unused parameters
IndrajeetPatil Apr 5, 2022
b023daf
Update DESCRIPTION
IndrajeetPatil Apr 5, 2022
39b2452
minor
IndrajeetPatil Apr 5, 2022
2d7affc
use `LabelConfiguration` for labels
IndrajeetPatil Apr 5, 2022
f6ce26e
add background configuration
IndrajeetPatil Apr 6, 2022
9d02de9
add an intermediary class
IndrajeetPatil Apr 6, 2022
b7bf095
Update plotIndividualTimeProfile.R
IndrajeetPatil Apr 6, 2022
d85b48b
update
IndrajeetPatil Apr 6, 2022
ae3f161
remove `createPlotConfiguration()`
IndrajeetPatil Apr 6, 2022
6e71242
use enums in docs
IndrajeetPatil Apr 7, 2022
680a6a4
choose defaults
IndrajeetPatil Apr 7, 2022
9f9b5b0
Merge branch 'develop' into 833_create_plot_configuration
IndrajeetPatil Apr 7, 2022
c4fc0cf
bump version of ospsuite.utils
IndrajeetPatil Apr 7, 2022
ddec561
minor
IndrajeetPatil Apr 7, 2022
28535a9
Merge branch 'develop' into 833_create_plot_configuration
IndrajeetPatil Apr 8, 2022
43230c6
defaults for export
IndrajeetPatil Apr 8, 2022
229b9d9
Merge branch 'develop' into old_plot_config
IndrajeetPatil Apr 12, 2022
983dd05
remove constructor; add aesthetics for annotations
IndrajeetPatil Apr 14, 2022
1eb8d0b
rename the class; adapt everything for this change
IndrajeetPatil Apr 14, 2022
2a2d4b9
no constructor needed for internal class either
IndrajeetPatil Apr 14, 2022
35c6e67
Merge branch 'develop' into old_plot_config
IndrajeetPatil Apr 14, 2022
f189839
rename file
IndrajeetPatil Apr 14, 2022
2e71925
choosing defaults
IndrajeetPatil Apr 14, 2022
dc519ec
minor
IndrajeetPatil Apr 14, 2022
30d2d1f
fix build failures
IndrajeetPatil Apr 14, 2022
9b17c2e
remaining substitutions
IndrajeetPatil Apr 19, 2022
bbb474a
remove options that don't make sense
IndrajeetPatil Apr 19, 2022
eed8bed
make the default `NULL`
IndrajeetPatil Apr 19, 2022
8b2ba31
Merge branch 'develop' into old_plot_config
IndrajeetPatil Apr 19, 2022
deb6045
remove unnecessary fields; catch up with tlf
IndrajeetPatil Apr 21, 2022
63436c4
more parameter cleanup
IndrajeetPatil Apr 25, 2022
33ae438
Merge branch 'develop' into old_plot_config
IndrajeetPatil Apr 25, 2022
76f55a6
Use ospDefault color map
IndrajeetPatil Apr 27, 2022
f5d8ac9
Merge branch 'develop' into old_plot_config
IndrajeetPatil Apr 27, 2022
fc39e11
Merge branch 'develop' into old_plot_config
IndrajeetPatil Apr 27, 2022
bf2dc24
remove spurious parameter
IndrajeetPatil Apr 27, 2022
802a3e3
Merge branch 'develop' into old_plot_config
IndrajeetPatil Apr 27, 2022
d90d84e
fix alignment issues
IndrajeetPatil Apr 29, 2022
027a1a9
non grouped datasets get their own grouping
IndrajeetPatil Apr 29, 2022
a035b09
fix color issue
IndrajeetPatil Apr 29, 2022
9d65a50
choose better axes default labels
IndrajeetPatil Apr 29, 2022
e0a3e15
respect user defined color maps as well
IndrajeetPatil Apr 29, 2022
8446686
Merge branch 'develop' into old_plot_config
IndrajeetPatil May 1, 2022
8dfd8a2
reduce size of axes labels; add example
IndrajeetPatil May 2, 2022
1ece6c0
add NEWS; move tlf to Suggests
IndrajeetPatil May 2, 2022
1b82a4e
can't re-export & have tlf in Suggests same time
IndrajeetPatil May 2, 2022
d3cff42
re-export for now
IndrajeetPatil May 2, 2022
52aa70f
more docs; tlf as hard dep; elementary class tests
IndrajeetPatil May 3, 2022
191e37f
add visual regression test
IndrajeetPatil May 3, 2022
564de4f
more enum; more tests
IndrajeetPatil May 3, 2022
3771f6e
skip for now
IndrajeetPatil May 3, 2022
1d97dcc
simplify updating legend data
IndrajeetPatil May 3, 2022
e12b3ba
first draft of `plotPopulationTimeProfile()`
IndrajeetPatil May 3, 2022
92af779
minor cleanup
IndrajeetPatil May 3, 2022
cf6227f
improve population profile plot
IndrajeetPatil May 4, 2022
79c78ba
also anticipate only observed/simulated contexts
IndrajeetPatil May 4, 2022
90c480f
anticipate missing error unit column
IndrajeetPatil May 4, 2022
9fd9196
support caption; try running tests on CI again
IndrajeetPatil May 5, 2022
a97dae1
tests for `plotIndividualTimeProfile()`
IndrajeetPatil May 5, 2022
bf11f6e
test for `plotPopulationTimeProfile()`
IndrajeetPatil May 5, 2022
9615deb
skip population test on AppVeyor
IndrajeetPatil May 5, 2022
81981cc
no unit in axes labels when unitless
IndrajeetPatil May 6, 2022
c66180c
use helper to remove duplicated code
IndrajeetPatil May 6, 2022
2350712
address more review comments
IndrajeetPatil May 6, 2022
05f64f4
not necessary anymore
IndrajeetPatil May 6, 2022
e912544
get rid of `DefaultInternalPlotConfiguration`
IndrajeetPatil May 6, 2022
887a921
separate linetype per dataset
IndrajeetPatil May 6, 2022
ac81da4
revert linetype change; anticipate other labels
IndrajeetPatil May 9, 2022
536d0d8
set default aesthetic maps on plot-by-plot basis
IndrajeetPatil May 10, 2022
0c213b7
closes https://github.com/Open-Systems-Pharmacology/OSPSuite-R/issues…
IndrajeetPatil May 11, 2022
3689730
docs
IndrajeetPatil May 11, 2022
a2471a1
More docs
IndrajeetPatil May 11, 2022
00f054f
section for scaling
IndrajeetPatil May 11, 2022
8769641
set tlf data to NULL when dataType isn't present
IndrajeetPatil May 11, 2022
84893cc
also update docs
IndrajeetPatil May 11, 2022
872da4f
Update plot-population-time-profile.R
IndrajeetPatil May 11, 2022
f672de5
add visual regression test for population profile
IndrajeetPatil May 11, 2022
1c85939
also test that changing linetypes works
IndrajeetPatil May 11, 2022
f0a732f
more docs
IndrajeetPatil May 11, 2022
8e052b9
extract out common plotting function
IndrajeetPatil May 11, 2022
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7 changes: 6 additions & 1 deletion DESCRIPTION
Original file line number Diff line number Diff line change
Expand Up @@ -30,7 +30,8 @@ Imports:
Suggests:
knitr,
rmarkdown,
testthat (>= 2.1.0)
testthat (>= 3.0.3),
vdiffr (>= 1.0.0)
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.2
Expand All @@ -49,6 +50,7 @@ Collate:
'data-importer-configuration.R'
'data-repository.R'
'data-set.R'
'default-plot-configuration.R'
'dot-net-wrapper.R'
'entity.R'
'formula.R'
Expand All @@ -70,6 +72,8 @@ Collate:
'pk-parameter-sensitivity.R'
'pk-parameter.R'
'pk-sim.R'
'plot-individual-time-profile.R'
'plot-population-time-profile.R'
'population-characteristics.R'
'population.R'
'quantity-pk-parameter.R'
Expand Down Expand Up @@ -109,6 +113,7 @@ Collate:
'utilities-pk-analysis.R'
'utilities-pk-parameter.R'
'utilities-pksim.R'
'utilities-plotting.R'
'utilities-population.R'
'utilities-quantity.R'
'utilities-sensitivity-analysis.R'
Expand Down
4 changes: 4 additions & 0 deletions NAMESPACE
Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,7 @@ export(DataCombined)
export(DataErrorType)
export(DataImporterConfiguration)
export(DataSet)
export(DefaultPlotConfiguration)
export(DotNetWrapper)
export(Gender)
export(HumanPopulation)
Expand Down Expand Up @@ -102,6 +103,8 @@ export(pkAnalysesToDataFrame)
export(pkAnalysesToTibble)
export(pkParameterByName)
export(plotGrid)
export(plotIndividualTimeProfile)
export(plotPopulationTimeProfile)
export(populationAsDataFrame)
export(populationToDataFrame)
export(populationToTibble)
Expand Down Expand Up @@ -138,6 +141,7 @@ export(validateUnit)
import(ospsuite.utils)
import(rClr)
import(tidyr)
import(tlf)
importFrom(ospsuite.utils,"%||%")
importFrom(ospsuite.utils,enum)
importFrom(ospsuite.utils,enumGetKey)
Expand Down
8 changes: 8 additions & 0 deletions NEWS.md
Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,14 @@
frame containing combined data from observed and simulated data, which can be
further used for visualizations or other analysis.

* Adds new visualization functions:

- `plotIndividualTimeProfile()` and `plotPopulationTimeProfile()` to create
time-profile plots.

* Adds a new class `DefaultPlotConfiguration` to provide plot configurations for
plotting functions.

* Adds `simulationResultsToDataFrame()` function to convert `SimulationResults`
objects into a data frame.

Expand Down
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