Version 1.3 #283
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Version 1.3 #283
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134 sensitivity plot
* Draft of a theme maker app * Include Wrapper for theme maker app * Remove data from internal package data For the examples and vignettes, external csv data seems much better and prevent corruption of RData types which crash R sometimes * Create smarter R6 Theme and related classes Also aesthetic properties are split in map and how the plots can use the map * Fixes and reconcile plot configuration with new theme workflow * Fixes atom plots with new plot configurations and themes Also errorbar has been redesigned * Provide user interface drafts for molecule plots The end goal is to also include them in vignettes * A test data set and theme template available in extdata * Fix boxplots with new theme configuration * Fix histograms with new theme configuration * Fix pk and ddi ratio plots with new theme configuration * Fix time profile and obs vs pred plots with new theme configuration * Throw a warning when data has no row in input * Provide default for all plot configurations * Update tornado plot * Add mapping defaults * Fix tests * Fix vignettes * Update namespace with the app wrappers * add example data and meta data in extdata * Fix vignette buidling fail * Remove theme from example in documentation * Fix background and plot configuration theme * Increment version 1.1 -> 1.2 * Import jsonlite in namespace This is necessary for RE to load its default theme * Make theme features cloneable and clone them within plot configurations If not cloned, theme and plot configurations are linked. Consequently, updating one object affects all of the others. * Fix setDefaultWatermark by not overwriting fonts if character
* Centralize all plots UI into one plot-maker called by runPlotMaker() * Use central sample data and fix some bugs for theme-maker * Fix DDI dataMapping types * Remove obsolete function * Fix bug in DDI ratio plot * Improve and fix some bugs of runPlotMaker() * Update news for tlf v1.2 * Improve and fix some bugs for runThemeMaker()
* Fixes #140 update tick size in plots using discrete scales * Fixes #141 enforce factors for legend and discrete scales of dataMapping * Fix copy/paste typo for ddi * Add plot maker options to read files other than csv and save plot Options include lines to skip and separator for read Saving option uses plot dimensions * Fix dataMapping comparison
* Create parsing functions to centralize common code chunks These functions return expressions which can be directly evaluated * Fixes #147 obs vs pred use PK ratio logic With this logic shapes and colors can be split in the legend Also, it is now possible to include uncertainty error bars * Simplify PK ratio plot based on the centralized parsing functions * DDI Ratio also benefit from PK Ratio and ObsVsPred logic * Use parsing functions in regular plots to centralize code * Fix plot tornado sort option * Updates on runPlotMaker * Simplify and improve options for file reading * Update helper text for aesthetic selection * Fix ggplot unwanted messages * Include new obs vs pred to plot maker * fix x and y axes limits in plot maker * styler * Update documentation based on check warnings * Provide a data selection input for runPlotMaker Convenient input if you don't want/need to use a full data.frame * Rename aaa.r to aaa-utilities.R describing better its content Update corresponding documentation
* Fixes #151 use coord_cartesian - `coord_trans()` can't be used for the transformation because the method adding the watermark in background. Consequently, log and discrete transformations still use scale_x/y... - For the same reason, `coord_cartesian()` is used to set the axis limits - suppressMessage is needed for the same reason as scale: multiple coord systems or scales lead to ggplot unwanted messages * Fix watermark size ggplot functions for labels and watermark do not use the same size unit. A conversion factor was used to fix that
* housekeeping - spell check - consistently use markdown syntax in roxygen docs - style - vignette chunk label fixes - minor rephrasing - update roxygen version - remove unnecessary pander from suggests - follow best practices for Rproject * edits to plot config vignette and sundry * edits to theme maker vignette * edits to the TLF workflow vignette * better chunk options * fix warnings from ggplot2 3.3.3 * revert ggplot2 version bump; spelling * edits to box plot vignette * edits to atom plots vignette * edits to PK ratio vignette
closes #164; rebuild website articles
* follows styling guidelines in vignettes * follows 80-character rule for roxygen docs
adding vignette urls to docs
Fix suggested from r-lib/pkgdown#1231
* Fixes #224 plotTimeProfile and its mapping are more versatile Now simulated and observed data can be plotted both independently or synchronized (as illustrated by vignette) with correct legend for both I also removed lloq from ObservedDataMapping that was making things complicated * Remove ggplot2 messages when aesthetic scales are updated * Export function to update time profile plot legend easily * Prevent time profile errors This code was a fix committed in PR #228 that may lead to a merge conflict
* Fixes #223 minimal theme is loaded and used by default * Remove theme loading from vignettes
* Fixes #231 legend key uses same color as legend background * Centralize update of legend features directly at plot initialization
* Fixes #216 Unit test result depends on the language settings * Install ospsuite.utils from github
* Fixes #234 add alignment as property of label objects Also fixes font family property in the process * Fixes #200 legend options for font and title are better defined * Account for the updates in the theme and plot UIs * Left align every label by default To get better display of final plots themes include the following alignments xticks, xlabel and ylabel are centered yticks are right aligned
* move plot grid function and class from ospsuite cf. Open-Systems-Pharmacology/OSPSuite-R#888 * remove references to ospsuite * Update PlotGridConfiguration.Rd * remove redundant test-coverage GHA
* add `$addPlots()` method to `PlotGridConfiguration` Closes #268 * add example * also anticipate single plot entered in a list * comment * more docs
* Add manual website in docs folder Closes #275 Removes github-actions, which are not working anyways * the rest * Update .Rbuildignore
* Bump package version; update NEWS * Also update website for new package version * rest * Update appveyor.yml
IndrajeetPatil
approved these changes
May 19, 2022
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