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Changelog

Source: vignettes/CHANGELOG.Rmd
CHANGELOG.Rmd

Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

Template for Changelog Entries

Each release section should follow the structure below:

[Version] - YYYY-MM-DD

Added
  • New features or functionality introduced in this release.
Changed
  • Updates or modifications to existing features.
Fixed
  • Bugs that have been resolved.
Deprecated
  • Features that are still functional but are slated for removal in the future.
Removed
  • Features or functionality that have been removed.
Security
  • Any security-related updates or patches.

Examples: - Added: Introduced a new plotting function plotTimeSeries(). - Fixed: Resolved an issue causing crashes when input data was missing values. - Changed: Modified the default parameters for normalizeData().

[0.1.3] - 2025-02-11

(In preparation)

Fixed
  • Bug that prevented the generation of the double spline plots when the condition column of meta was a factor instead of a string. This is now solved (it internally in the code converts it to a string), so having the condition column as a factor now does not cause problems anymore (as having it as factor is perfectly valid).

[0.1.2] - 2025-02-11

Added
  • Level name in title of overall spline plots.
Fixed
  • Small bug that made it impossible having no treatment label for a condition.
  • Small bug that did not allow to specify two treatment labels.
  • mode == isolated for RNA-seq data. Before, it caused an error, because it splits up the meta into the different conditions, but does not do so for the data. Now, it informs the user that it cannot do this, and the user has to split up the data himself outside (just for RNA-seq data).
Removed
  • open_template() function. This was a function that opened a template for your own analysis. I removed it, because otherwise, whenever I change the code, I have to update the get-started vignette (tutorial) and this, which is twice the maintainance effort.

[0.1.1] - 2025-01-29

Changed

  • The design formula must now contain the string ‘Time’ rather than ‘X’ like it was before. X from before stood for the time. This change is intended to make the design formula more explicit and self explanatory.
  • Random effects can now be directly be specified in the design formula, rather than being passed as part of the dream_params.

Added

  • Added linear mixed models for modeling random effects. The variancePartition package is used for that –> voomWithDreamWeights for RNA-seq data processing, and dream as the replacement for limma. For example, if you Reactor is your random effect, you can write the design formula like this: design <- “~ 1 + Condition*Time + Plate + (1|Reactor)” and SplineOmics will automatically run the variancePartition functions voomWithDreamWeights() and dream() instead of the limma::voom and lmfit. dream() has additional parameters, such as the method and the degree of freedom (different than the degree of freedom used for the splines in this package) and you can pass these with the dream_params argument. See RNA-seq analysis vignette or the respective function references for more info.
  • Raw data plotting function –> make_scatter_plot_html() –> see references.
  • Imputed values are marked with triangle symbols in cluster_hits() spline plots if raw data is passed.
  • Package version is written in each HTML report (the tag) and the session info is added as an embedded text file.
  • Standard error written on top of “double spline” plots (limma result category 2 and 3).
  • Used analysis script is embedded as a text file in the reports.
  • The mode (integrated or isolated) is written on top of the reports in a separate field.
  • Now there are 4 significance stars.
  • Treatment lines for the double spline plots (limma result category 2 and 3).
Fixed
  • A few smaller visual things for the HTML reports.

Session Info 

## R version 4.3.3 (2024-02-29)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 22.04.5 LTS
## 
## Matrix products: default
## BLAS:   /usr/local/R-4.3.3/lib/R/lib/libRblas.so 
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=de_AT.UTF-8        LC_COLLATE=en_US.UTF-8    
##  [5] LC_MONETARY=de_AT.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=de_AT.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=de_AT.UTF-8 LC_IDENTIFICATION=C       
## 
## time zone: Europe/Vienna
## tzcode source: system (glibc)
## 
## attached base packages:
## [1] stats     graphics  grDevices datasets  utils     methods   base     
## 
## loaded via a namespace (and not attached):
##  [1] digest_0.6.37       desc_1.4.3          R6_2.6.1           
##  [4] fastmap_1.2.0       xfun_0.50           cachem_1.1.0       
##  [7] knitr_1.49          htmltools_0.5.8.1   rmarkdown_2.29     
## [10] lifecycle_1.0.4     cli_3.6.4           sass_0.4.9         
## [13] pkgdown_2.1.1       textshaping_1.0.0   jquerylib_0.1.4    
## [16] renv_1.1.1          systemfonts_1.2.1   compiler_4.3.3     
## [19] rstudioapi_0.17.1   tools_4.3.3         ragg_1.3.3         
## [22] bslib_0.9.0         evaluate_1.0.3      yaml_2.3.10        
## [25] BiocManager_1.30.25 jsonlite_1.8.9      htmlwidgets_1.6.4  
## [28] rlang_1.1.5         fs_1.6.5