Version 0.5.1 enhances the density based statistics with several new features without changing their default behaviour. The aim is to add flexibility better supporting the creation of annotated volcano and quadrant plots. These types of plots are frequently used to present gene transcript abundance estimates obtained by RNAseq or microarrays.
Tag: plotting
ggpmisc 0.5.2
Version 0.5.2 fixes several bugs.
ggpp 0.5.0
Version 0.5.0 includes code-breaking enhancements to geom_text_s() and geom_label_s(). The most significative is a mechanism to selectively applying aesthetics to different components of linked labels and text. This replaces the previous use of separate aesthetics applied only to segments or arrows. The reason behind this change is that segments are only links, and not meant to inform about data values on their own.
ggpmisc 0.5.1
Version 0.5.1 brings additional enhancements to the annotations based on model fits. These enhancements improve traceability by updating statistics to return additional information about the fitted models. Functions in ‘ggplot2’ that had been earlier announced as being at their end-of-life have now been deprecated. Some instances aes_() had remained lingering in the code and had to be replaced by aes() .
ggpp 0.4.5
Version 0.4.5 includes fixes for compatibility with the upcoming updates in ‘ggplot2’ version 3.4.0, and adds enhancements to geom_text_s() and geom_label_s(). The most significative is the computation of the justification from the position displacement, which works with any of the position functions exported by ‘ggpp’. Another significant change is the implementation of padding.
ggpmisc 0.5.0
Version 0.5.0 (previously announced as 0.4.8) brings enhancements to the annotations based on model fits. The most significant change for all users is the new convenience function use_label() that greatly simplifies the assembly of labels from components and their mapping to aesthetics. We examplify its use and some of the other new features. It also contains two changes that are not backwards compatible and that can in isolated cases break existing code (hence the version-number change into 0.5.0).
ggpmisc 0.4.7
Version 0.4.7 brings a fix for a bug that could prevent the use of weights passed through aesthetic weight in some of the model-fitting statistics. Several enhancements to the model fitting statistics make it easier to fit different models to different groups or panels, and make it possible/easier to select among methods supported by a model fit function.
ggpp 0.4.4
Version 0.4.4 fixes a bug affecting most of the geometries in the package. Adding multiple layers using the same geom to the same plot would result in only one of these layers being rendered with others silently missing from the graphical output.
Changes compared to version 0.4.3, the previous version in CRAN are:
- Fix bug caused by repeated grob and grob tree names.
Documentation web site at http://docs.r4photobiology.info/ggpp/ includes all help pages, with output from all examples, vignettes as well as a changelog in HTML format.
NOTE: Version 0.4.4 is on its way to CRAN.
Please raise issues concerning bugs or enhancements to this package through GitHub at https://github.com/aphalo/ggpp/issues. Pull requests are also welcome.
ggpmisc 0.4.6
Version 0.4.6 fixes a significant bug occasionally affecting highlighting and labelling of peaks and valleys. Even though when triggered the problem is easily detectable by looking at the plot, please, update.
Changes compared to version 0.4.5, the previous version in CRAN are:
- Fix bug in
stat_peaks() and stat_valleys(). They could return wrong values for peaks and valleys if the rows in data in the ggplot object were not sorted by the value of x.
Documentation web site at http://docs.r4photobiology.info/ggpmisc/ includes all help pages, with output from all examples, vignettes as well as a changelog in HTML format.
NOTE: Version 0.4.6 is on its way to CRAN.
Please raise issues concerning bugs or enhancements to this package through GitHub https://github.com/aphalo/ggpmisc/issues
ggpp 0.4.3
Functions included in this update provide enhamcements on existing ones. Combining nudging with stack, jitter and dodge positions was not possible within the grammar of graphics as implemented in package ‘ggplot2’. This made it difficult to add data labels to some types of plots. Which for example, can be important in plots aimed at audiences outside academia. These functions are based, with permission, on code written by M. Krassowski in the GitHub repository for ‘ggrepel’.
Other new position functions with names ending in _keep, for which normal counterparts exist, keep the original position in data, allowing the drawing of connecting segments with the geometries from package ‘ggrepel’ and with the updated geometries in ‘ggpp’.
ggpmisc 0.4.5
Version 0.4.5 includes a minor bugfix and an edit in vignette examples, to ensure compatibility with the upcoming version of package ‘ggpp’.
Changes compared to version 0.4.4, the previous version in CRAN are:
- Decrease version of ‘gginnards’ in suggests.
- Edit vignette examples to allow renaming a geom exported by ‘ggpp’ (retaining backwards compatibility).
Documentation web site at http://docs.r4photobiology.info/ggpmisc/ includes all help pages, with output from all examples, vignettes as well as a changelog in HTML format.
NOTE: Version 0.4.5 is on its way to CRAN.
Please raise issues concerning bugs or enhancements to this package through GitHub https://github.com/aphalo/ggpmisc/issues
ggpmisc 0.4.4
Version 0.4.4 includes enhancements. An issue raised in GitHub and a question in StackOverflow asked for the possibility of changing how fitted lines are plotted based on the “goodness” of the fit. In addition an old question in StackOverflow highlighted the need of more intuitive support for annotations based on stats::cor.test(). In addition to implementing these enhancements we continued adding support for flipping of statistics controlled through formal parameter orientation as implemented in ‘ggplot2’ since version 3.3.0.
Changes compared to version 0.4.3, the previous version in CRAN are:
- Add new function
stat_correlation() to annotate plots with correlation estimates, their P-value, a test statistic and n computed with stats::cor.test(). In addition to formatted character strings, numeric values are included in the returned data frame to facilitate conditional display.
- Update
stat_poly_line() to optionally add columns n, p.value, r.squared , adj.r.squared and method to the returned data frame. Code breaking: This statistic no longer supports fitting of splines with methods such as loess . This could potentially break user code, in which case the solution is to use stat_smooth().
- Update
stat_ma_line() to optionally add columns n, p.value, r.squared and method to the returned data frame. (As only a slope can be fitted, adj.r.squared is irrelevant.)
- Update
stat_quant_line() and stat_quant_band() to optionally add n and method columns to the returned data frame. (No exact equivalent of r.squared exists for quantile regression.)
- Update
stat_fit_residuals() to optionally return weighted
residuals.
- Update
stat_peaks() and stat_valleys() to allow flipping with new parameter orientation.
Documentation web site at http://docs.r4photobiology.info/ggpmisc/ includes all help pages, with output from all examples, vignettes as well as a changelog in HTML format.
NOTE: Version 0.4.4 is on its way to CRAN.
Please raise issues concerning bugs or enhancements to this package through GitHub https://github.com/aphalo/ggpmisc/issues
ggpmisc 0.5.2
Version 0.5.2 fixes several bugs.
ggpp 0.5.0
Version 0.5.0 includes code-breaking enhancements to geom_text_s() and geom_label_s(). The most significative is a mechanism to selectively applying aesthetics to different components of linked labels and text. This replaces the previous use of separate aesthetics applied only to segments or arrows. The reason behind this change is that segments are only links, and not meant to inform about data values on their own.
ggpmisc 0.5.1
Version 0.5.1 brings additional enhancements to the annotations based on model fits. These enhancements improve traceability by updating statistics to return additional information about the fitted models. Functions in ‘ggplot2’ that had been earlier announced as being at their end-of-life have now been deprecated. Some instances aes_() had remained lingering in the code and had to be replaced by aes() .
ggpp 0.4.5
Version 0.4.5 includes fixes for compatibility with the upcoming updates in ‘ggplot2’ version 3.4.0, and adds enhancements to geom_text_s() and geom_label_s(). The most significative is the computation of the justification from the position displacement, which works with any of the position functions exported by ‘ggpp’. Another significant change is the implementation of padding.
ggpmisc 0.5.0
Version 0.5.0 (previously announced as 0.4.8) brings enhancements to the annotations based on model fits. The most significant change for all users is the new convenience function use_label() that greatly simplifies the assembly of labels from components and their mapping to aesthetics. We examplify its use and some of the other new features. It also contains two changes that are not backwards compatible and that can in isolated cases break existing code (hence the version-number change into 0.5.0).
ggpmisc 0.4.7
Version 0.4.7 brings a fix for a bug that could prevent the use of weights passed through aesthetic weight in some of the model-fitting statistics. Several enhancements to the model fitting statistics make it easier to fit different models to different groups or panels, and make it possible/easier to select among methods supported by a model fit function.
ggpp 0.4.4
Version 0.4.4 fixes a bug affecting most of the geometries in the package. Adding multiple layers using the same geom to the same plot would result in only one of these layers being rendered with others silently missing from the graphical output.
Changes compared to version 0.4.3, the previous version in CRAN are:
- Fix bug caused by repeated grob and grob tree names.
Documentation web site at http://docs.r4photobiology.info/ggpp/ includes all help pages, with output from all examples, vignettes as well as a changelog in HTML format.
NOTE: Version 0.4.4 is on its way to CRAN.
Please raise issues concerning bugs or enhancements to this package through GitHub at https://github.com/aphalo/ggpp/issues. Pull requests are also welcome.
ggpmisc 0.4.6
Version 0.4.6 fixes a significant bug occasionally affecting highlighting and labelling of peaks and valleys. Even though when triggered the problem is easily detectable by looking at the plot, please, update.
Changes compared to version 0.4.5, the previous version in CRAN are:
- Fix bug in
stat_peaks()andstat_valleys(). They could return wrong values for peaks and valleys if the rows indatain the ggplot object were not sorted by the value of x.
Documentation web site at http://docs.r4photobiology.info/ggpmisc/ includes all help pages, with output from all examples, vignettes as well as a changelog in HTML format.
NOTE: Version 0.4.6 is on its way to CRAN.
Please raise issues concerning bugs or enhancements to this package through GitHub https://github.com/aphalo/ggpmisc/issues
ggpp 0.4.3
Functions included in this update provide enhamcements on existing ones. Combining nudging with stack, jitter and dodge positions was not possible within the grammar of graphics as implemented in package ‘ggplot2’. This made it difficult to add data labels to some types of plots. Which for example, can be important in plots aimed at audiences outside academia. These functions are based, with permission, on code written by M. Krassowski in the GitHub repository for ‘ggrepel’.
Other new position functions with names ending in _keep, for which normal counterparts exist, keep the original position in data, allowing the drawing of connecting segments with the geometries from package ‘ggrepel’ and with the updated geometries in ‘ggpp’.
ggpmisc 0.4.5
Version 0.4.5 includes a minor bugfix and an edit in vignette examples, to ensure compatibility with the upcoming version of package ‘ggpp’.
Changes compared to version 0.4.4, the previous version in CRAN are:
- Decrease version of ‘gginnards’ in suggests.
- Edit vignette examples to allow renaming a geom exported by ‘ggpp’ (retaining backwards compatibility).
Documentation web site at http://docs.r4photobiology.info/ggpmisc/ includes all help pages, with output from all examples, vignettes as well as a changelog in HTML format.
NOTE: Version 0.4.5 is on its way to CRAN.
Please raise issues concerning bugs or enhancements to this package through GitHub https://github.com/aphalo/ggpmisc/issues
ggpmisc 0.4.4
Version 0.4.4 includes enhancements. An issue raised in GitHub and a question in StackOverflow asked for the possibility of changing how fitted lines are plotted based on the “goodness” of the fit. In addition an old question in StackOverflow highlighted the need of more intuitive support for annotations based on stats::cor.test(). In addition to implementing these enhancements we continued adding support for flipping of statistics controlled through formal parameter orientation as implemented in ‘ggplot2’ since version 3.3.0.
Changes compared to version 0.4.3, the previous version in CRAN are:
- Add new function
stat_correlation()to annotate plots with correlation estimates, their P-value, a test statistic and n computed withstats::cor.test(). In addition to formatted character strings, numeric values are included in the returned data frame to facilitate conditional display. - Update
stat_poly_line()to optionally add columnsn,p.value,r.squared,adj.r.squaredandmethodto the returned data frame. Code breaking: This statistic no longer supports fitting of splines with methods such asloess. This could potentially break user code, in which case the solution is to usestat_smooth(). - Update
stat_ma_line()to optionally add columnsn,p.value,r.squaredandmethodto the returned data frame. (As only a slope can be fitted,adj.r.squaredis irrelevant.) - Update
stat_quant_line()andstat_quant_band()to optionally addnandmethodcolumns to the returned data frame. (No exact equivalent ofr.squaredexists for quantile regression.) - Update
stat_fit_residuals()to optionally return weighted
residuals. - Update
stat_peaks()andstat_valleys()to allow flipping with new parameterorientation.
Documentation web site at http://docs.r4photobiology.info/ggpmisc/ includes all help pages, with output from all examples, vignettes as well as a changelog in HTML format.
NOTE: Version 0.4.4 is on its way to CRAN.
Please raise issues concerning bugs or enhancements to this package through GitHub https://github.com/aphalo/ggpmisc/issues
