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Improvements to the PlotGridConfiguration
class
#293
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PlotGridConfiguration
class
Print output: library(tlf)
set.seed(123)
ls_plots <- list(
# first plot
plotBoxWhisker(mtcars,
dataMapping = BoxWhiskerDataMapping$new(x = "am", y = "wt"), outliers = FALSE
),
# second plot
plotBoxWhisker(ToothGrowth,
dataMapping = BoxWhiskerDataMapping$new(x = "supp", y = "len")
)
)
plotGridObj <- PlotGridConfiguration$new(ls_plots)
plotGridObj$title <- "my combined plot"
plotGridObj$subtitle <- "something clever"
plotGridObj$caption <- "something dumb"
plotGridObj$nColumns <- 2L
plotGridObj$nRows <- 1L
plotGridObj$byRow <- TRUE
plotGridObj$tagLevels <- "A"
plotGridObj$tagPrefix <- "Plot ("
plotGridObj$tagSuffix <- ")"
plotGridObj
#> PlotGridConfiguration:
#> Plot grid annotations:
#> Title: my combined plot
#> Subtitle: something clever
#> Caption: something dumb
#> Plot grid arrangement:
#> Number of plots included: 2
#> Number of columns in the grid: 2
#> Number of rows in the grid: 1
#> Arranged in row-major order: TRUE
#> Individual plot tags:
#> Tag level format: A
#> Tag level prefix: Plot (
#> Tag level suffix: )
#> Tag level separator: Created on 2022-05-24 by the reprex package (v2.0.1.9000) |
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PlotGridConfiguration
classPlotGridConfiguration
class
- Add needed enums - Update NEWS for the same - Update docs - Add test - Update examples
library(ggplot2)
library(tlf)
# plots to be arranged in a grid
set.seed(123)
ls_plots <- list(
plotHistogram(x = rnorm(100)),
plotHistogram(x = rnorm(100, mean = 3)),
plotHistogram(x = rnorm(100, mean = 10))
)
# create an instance of plot configuration class
plotGridObj <- PlotGridConfiguration$new(plotList = ls_plots)
# specify further customizations for the plot grid
plotGridObj$title <- "my combined plot"
plotGridObj$subtitle <- "something clever"
plotGridObj$caption <- "my sources"
plotGridObj$nColumns <- 2L
plotGridObj$tagLevels <- "A"
plotGridObj$tagPrefix <- "Plot ("
plotGridObj$tagSuffix <- ")"
plotGridObj$tagColor <- "orange"
plotGridObj$tagSize <- 15
plotGridObj$tagAngle <- 45
plotGridObj$tagPosition <- TagPositions$top
plotGridObj$titleColor <- "darkgreen"
plotGridObj$subtitleColor <- "darkred"
plotGridObj$captionColor <- "blue"
plotGridObj$captionSize <- 12
plotGridObj$titleHorizontalJustification <- HorizontalJustification$middle
plotGridObj$subtitleHorizontalJustification <- HorizontalJustification$middle
plotGridObj$captionHorizontalJustification <- HorizontalJustification$middle
# plot the grid
plotGrid(plotGridObj) Created on 2022-05-24 by the reprex package (v2.0.1.9000) |
Codecov Report
@@ Coverage Diff @@
## develop #293 +/- ##
===========================================
+ Coverage 57.79% 64.28% +6.48%
===========================================
Files 51 51
Lines 2827 2878 +51
===========================================
+ Hits 1634 1850 +216
+ Misses 1193 1028 -165
Continue to review full report at Codecov.
|
Package: tlf | ||
Type: Package | ||
Title: TLF Library | ||
Version: 1.4.0 |
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@Yuri05 Bumping the version. Is that okay?
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Yes :)
@@ -12,10 +12,10 @@ install: | |||
- git submodule update --init --recursive | |||
|
|||
environment: | |||
app_version: "1.3" | |||
app_version: "1.4" |
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@Yuri05 Same as DESCRIPTION
USE_RTOOLS: true | ||
R_ARCH: x64 | ||
R_VERSION: "4.0.5" | ||
R_VERSION: "4.1.0" |
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So that visual regression tests can run on AppVeyor
R/plot-grid.R
Outdated
title = NULL, | ||
titleColor = "black", | ||
titleSize = 14, |
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don't we have this (and other sizes below) as a constant somewhere in the tlf?
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No, but I have created an enum for it now.
# ****IMPORTANT** | ||
# | ||
# Do not move these enums to any other file! | ||
# | ||
# R6 class generators will create classes at build time. This means that if any | ||
# of the enums are to be used inside these class environments, they need to be | ||
# already available in the NAMESPACE when classes are being created. If not, you | ||
# will get "object not found" error because R6 class generator can't find these | ||
# enums in the NAMESPACE. | ||
# | ||
# This whole problem can be easily avoided by collating NAMESPACE alphabetically | ||
# and including the enums in `aaa-` file which will be loaded before all other | ||
# files and therefore all R6 class environments can find the needed enums since | ||
# these classes will be defined in these other files. |
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@pchelle Please make note of this. I have moved all enums to a single file now.
I need to some more research into this, but keeping them in a single file is a good solution at the moment.
@Yuri05 I have made the changes you had asked. Let me know if you want me to change anything else. |
Change the world :) |
* Fixes #280 background elements defined a priori (#284) This allows to switch off grid at creation of plot configuration * Fixes #281 Fixes #282 update vignettes (#290) * Fixes #289 update news (#291) * 273 na rm (#278) * Fixes #273 NA are removed without producing warnings * Fixes #272 set transparency for molecular plots * Update line layer in scatter plots * Fix typo Co-authored-by: Indrajeet Patil <[email protected]> * Fixes #288 create sections in reference page of doc website (#292) * Fixes #288 create sections in reference page of doc website * Remove duplicated last reference section * Export configuration output folder (#287) * Add `path` property to `ExportConfiguration` * Added argument `path` to `ExportConfiguration` Documentation generated with roxygen2 * Run styler * Fix wrong assignment of `path` property * adopt same gitattributes as other R repos in OSP (#295) * whitespace changes due to new gitattributes * Improvements to the `PlotGridConfiguration` class (#293) * Bump package version; update NEWS * Also update website for new package version * rest * Update appveyor.yml * Add print method for plot grid config Closes #274 * document * better example * better headers * add more aesthetic parameters for plot grid config - Add needed enums - Update NEWS for the same - Update docs - Add test - Update examples * style * caption position * bump version * Add PlotAnnotationTextSize * move enums to plot grid file * docs * Update PlotGridConfiguration.Rd * needed for vdiffr tests * move all enums to their own file * also add watermark size to the enum (#297) * whitespace changes due to new gitattributes * Use utilities from ospsuite.utils (#299) To be considered once Open-Systems-Pharmacology/OSPSuite.RUtils#115 is merged. * Add `collate` directive (#296) * Fixes #301 Helper function to get lines from fold distance values (#302) * Fixes #301 Helper function to get lines from fold distance values * Update news, doc and style * Update NEWS.md * Update NEWS.md Co-authored-by: Indrajeet Patil <[email protected]> * 262 res vs pred (#270) * Fixes #262 update documentation of plotResVsPred * Fixes #262 res vs time functions are aliases of res vs pred functions Include plotResVsTime, ResVsTimePlotConfiguration and ResVsTimeDataMapping * res vs time classes derive from res vs pred As a consequence, they are not equal and can have different theme properties * re-document Co-authored-by: Indrajeet Patil <[email protected]> * Fixes #304 add enum helper for ticklabels (#305) * Fixes #304 add enum helper for ticklabels * Fix typo in Pi label mapping * Fix typo in example * If ticklabels is of type expression, numeric or function use it as is If expression or function isIncluded throw an error so the assertion is necessary before isIncluded * style and document Co-authored-by: Indrajeet Patil <[email protected]> * Prepend internal function names with a dot (#307) As per coding guidelines. Update docs for these functions as well. Closes #306 * 308 fold distance (#311) * Fixes #313 Remove badges from Website-docu, update news (#314) Co-authored-by: Yuri05 <[email protected]> * Fixes #260 legend titles are updated and can be defined in themes (#315) * Fixes #260 legend titles are updated and can be defined in themes * Remove legend and legend title reset in boxplots * Fixes #312 remove infinite values from plots (#316) * fixes #318 Update website (#319) Co-authored-by: Yuri05 <[email protected]> * Fixes #320 Website: some images not displayed (#321) Co-authored-by: Yuri05 <[email protected]> * 320 attempt2 (#322) * delete old docs folder * Fixes #320 Website: some images not displayed Co-authored-by: Yuri05 <[email protected]> Co-authored-by: Pierre Chelle <[email protected]> Co-authored-by: Indrajeet Patil <[email protected]> Co-authored-by: Pavel Balazki <[email protected]> Co-authored-by: Yuri05 <[email protected]>
…acology#293) * Bump package version; update NEWS * Also update website for new package version * rest * Update appveyor.yml * Add print method for plot grid config Closes Open-Systems-Pharmacology#274 * document * better example * better headers * add more aesthetic parameters for plot grid config - Add needed enums - Update NEWS for the same - Update docs - Add test - Update examples * style * caption position * bump version * Add PlotAnnotationTextSize * move enums to plot grid file * docs * Update PlotGridConfiguration.Rd * needed for vdiffr tests * move all enums to their own file
* Version 1.4.89 (#323) * Fixes #280 background elements defined a priori (#284) This allows to switch off grid at creation of plot configuration * Fixes #281 Fixes #282 update vignettes (#290) * Fixes #289 update news (#291) * 273 na rm (#278) * Fixes #273 NA are removed without producing warnings * Fixes #272 set transparency for molecular plots * Update line layer in scatter plots * Fix typo Co-authored-by: Indrajeet Patil <[email protected]> * Fixes #288 create sections in reference page of doc website (#292) * Fixes #288 create sections in reference page of doc website * Remove duplicated last reference section * Export configuration output folder (#287) * Add `path` property to `ExportConfiguration` * Added argument `path` to `ExportConfiguration` Documentation generated with roxygen2 * Run styler * Fix wrong assignment of `path` property * adopt same gitattributes as other R repos in OSP (#295) * whitespace changes due to new gitattributes * Improvements to the `PlotGridConfiguration` class (#293) * Bump package version; update NEWS * Also update website for new package version * rest * Update appveyor.yml * Add print method for plot grid config Closes #274 * document * better example * better headers * add more aesthetic parameters for plot grid config - Add needed enums - Update NEWS for the same - Update docs - Add test - Update examples * style * caption position * bump version * Add PlotAnnotationTextSize * move enums to plot grid file * docs * Update PlotGridConfiguration.Rd * needed for vdiffr tests * move all enums to their own file * also add watermark size to the enum (#297) * whitespace changes due to new gitattributes * Use utilities from ospsuite.utils (#299) To be considered once Open-Systems-Pharmacology/OSPSuite.RUtils#115 is merged. * Add `collate` directive (#296) * Fixes #301 Helper function to get lines from fold distance values (#302) * Fixes #301 Helper function to get lines from fold distance values * Update news, doc and style * Update NEWS.md * Update NEWS.md Co-authored-by: Indrajeet Patil <[email protected]> * 262 res vs pred (#270) * Fixes #262 update documentation of plotResVsPred * Fixes #262 res vs time functions are aliases of res vs pred functions Include plotResVsTime, ResVsTimePlotConfiguration and ResVsTimeDataMapping * res vs time classes derive from res vs pred As a consequence, they are not equal and can have different theme properties * re-document Co-authored-by: Indrajeet Patil <[email protected]> * Fixes #304 add enum helper for ticklabels (#305) * Fixes #304 add enum helper for ticklabels * Fix typo in Pi label mapping * Fix typo in example * If ticklabels is of type expression, numeric or function use it as is If expression or function isIncluded throw an error so the assertion is necessary before isIncluded * style and document Co-authored-by: Indrajeet Patil <[email protected]> * Prepend internal function names with a dot (#307) As per coding guidelines. Update docs for these functions as well. Closes #306 * 308 fold distance (#311) * Fixes #313 Remove badges from Website-docu, update news (#314) Co-authored-by: Yuri05 <[email protected]> * Fixes #260 legend titles are updated and can be defined in themes (#315) * Fixes #260 legend titles are updated and can be defined in themes * Remove legend and legend title reset in boxplots * Fixes #312 remove infinite values from plots (#316) * fixes #318 Update website (#319) Co-authored-by: Yuri05 <[email protected]> * Fixes #320 Website: some images not displayed (#321) Co-authored-by: Yuri05 <[email protected]> * 320 attempt2 (#322) * delete old docs folder * Fixes #320 Website: some images not displayed Co-authored-by: Yuri05 <[email protected]> Co-authored-by: Pierre Chelle <[email protected]> Co-authored-by: Indrajeet Patil <[email protected]> Co-authored-by: Pavel Balazki <[email protected]> Co-authored-by: Yuri05 <[email protected]> * Improvements to the `PlotGridConfiguration` class (#293) * Bump package version; update NEWS * Also update website for new package version * rest * Update appveyor.yml * Add print method for plot grid config Closes #274 * document * better example * better headers * add more aesthetic parameters for plot grid config - Add needed enums - Update NEWS for the same - Update docs - Add test - Update examples * style * caption position * bump version * Add PlotAnnotationTextSize * move enums to plot grid file * docs * Update PlotGridConfiguration.Rd * needed for vdiffr tests * move all enums to their own file * also add watermark size to the enum (#297) * Fixes #301 Helper function to get lines from fold distance values (#302) * Fixes #301 Helper function to get lines from fold distance values * Update news, doc and style * Update NEWS.md * Update NEWS.md Co-authored-by: Indrajeet Patil <[email protected]> * Fixes #304 add enum helper for ticklabels (#305) * Fixes #304 add enum helper for ticklabels * Fix typo in Pi label mapping * Fix typo in example * If ticklabels is of type expression, numeric or function use it as is If expression or function isIncluded throw an error so the assertion is necessary before isIncluded * style and document Co-authored-by: Indrajeet Patil <[email protected]> * 308 fold distance (#311) * 320 attempt2 (#322) * delete old docs folder * Fixes #320 Website: some images not displayed Co-authored-by: Yuri05 <[email protected]> * Fixes #325 legend title properties from argument title are used (#328) Issue was caused because properties of R6 (Label object here) are linked if object is not cloned * Fixes #327 horizontal bars for obs vs pred plots (#331) - error is replaced in favor of ymin/ymax or xmin/xmax - dataMapping initialize method needs to explicitly redefine `x` and `y` arguments because of R partial matching (if user inputs `x="a"`, partial matching would assign "a" to `xmin` instead of `x` because `xmin` was the only argument explicitly defined) * Refresh README (#335) * Refresh README Closes #153 Closes #334 * remove README.Rmd * Update README.md * Classify vignettes on the website (#336) Closes #178 * Make `.Rbuildignore` more comprehensive (#337) * Make `.Rbuildignore` more comprehensive Get rid of `NOTE` about unexpected top-level files * Update .Rbuildignore * Update to roxygen2 7.2.1 (#339) * Format with latest version of styler (#341) * Fixes #326 legend title use plot configuration for time profile plots (#343) * Get rid of warnings and notes in R CMD check (#338) * Fixes #333 set cap width of errorbars (#344) * Fixes #333 set cap width of errorbars Currently, width is a global setting applied the same way to all error bars * Absolute cap values are now relative and width renamed to extent Renaming width to extent to prevent user confusion when used for horizontal errorbars whose caps become vertical * Fixes #333 cap extent renamed cap size and use consistent unit in pts Co-authored-by: Indrajeet Patil <[email protected]> * 303 obs map to shape (#351) * Fixes #303 observed data map to shape * Fixes #346 remove dynamic code * Update documentation with latest roxygen * format with styler Co-authored-by: Indrajeet Patil <[email protected]> * Fixes #353 time profile legend guide display and order shapes (#355) * Fixes #356 display minor ticks (#357) * Fixes #356 display minor ticks * fix test Co-authored-by: Indrajeet Patil <[email protected]> * Fixes #354 ObservedDataMapping signature consistent with TimeProdfle (#358) * Fixes #360 add linetype as internal splitting group for simulation range (#361) * Fixes #350 default obs vs pred plot use same axes limits (#365) The same option also centers residuals vs pred/time around 0 * format with {styler} (#366) * Fixes #368 Add identity in Scaling enum (#371) Also fix a typo in enum Shapes * Fixes #375 Add spellcheck * Fixes #362 introduce qq plots (#370) * Fixes #362 introduce qq plots * Remove empty y check overkill Co-authored-by: Indrajeet Patil <[email protected]> * Fixes #364 introduce cumulative time profile plots (#378) * 374 enum listing molecules (#380) * Fixes #375 enums listing all molecules, atoms and their configurations * Fixes #379 Synchronize theme and molecule plots * Rename Atoms and Molecules to AtomPlots and MoleculePlots * Fixes #381 Prevent log ticks from crashing plots (#382) * Fixes #387 enforce factor type to prevent crash of colorBreaks (#388) levels of character type variable is null possibly leading to null colorBreaks value * Fixes #383 histogram can plot bars as frequency (#384) * Fixes #383 histogram can plot bars as frequency * Update documentation about default values of histogram * Fixes #390 Fixes #391 observed and simulated time profiles (#393) * Fixes #392 Create method for dual axis time profile plots (#396) * Fixes #392 Create method for dual axis time profile plots * Update test plot grid snapshot to latest * Fixes #398 update documentation and website (#399) * Fixes #398 update documentation and website * Fixes #398 Update version and dev documentation * Update release documentation * Fixes #397 vignette code is run only if R version is >= 4.0 (#401) * Increment AppVeyour version (1.4=>1.5) (#402) Co-authored-by: Yuri05 <[email protected]> * merge main into develop --------- Co-authored-by: Michael Sevestre <[email protected]> Co-authored-by: Pierre Chelle <[email protected]> Co-authored-by: Indrajeet Patil <[email protected]> Co-authored-by: Pavel Balazki <[email protected]> Co-authored-by: Yuri05 <[email protected]>
print
forPlotGridConfiguration
#274PlotGridConfiguration
class to control tag aesthetics #294