# Changelog

Source: `NEWS.md`

# DTUrtle 1.0.2

## Changes

- `plot_transcripts_view()`: now creates missing save folder, like other plotting functions.
- `check_unique_by_partition()`: now handles columns with only `NA` values.
- `get_by_partition()`: correctly retains factor columns.
- styled R code with `styler`-package for better code readability.

# DTUrtle 1.0.1

## Changes

- filtering confusing DRIMSeq computation time messages.
  - implemented a message filtering function `filter_messages()`.
- `plot_transcripts_view()`: added `include_ID_in_title` parameter.
- `plot_proportion_barplot()`: added `label_angle` parameter.
- added `lifecycle` and `R build status` badges.
  - added automatic `R CMD check` via GitHub actions.
- moved general package code from `zzz.R` to `DTUrtle-package.R`.
- new Suggests: `lifecycle`

# DTUrtle 1.0.0

## Changes

- DTUrtle manuscript got published in Bioinformatics:
  - added citation information.
  - added DOI in Readme.

# DTUrtle 0.8.1

## Changes

- remodeled a lot of code - preserving functionality if not stated otherwise.
- added basic DGE-calling methods:
  - `import_dge_counts()`: import quantification data and summarize to gene-level.
  - `run_deseq2()`: perform DGE analysis with DESeq2.
- added `priming_bias_detection_probability()` functionality, to estimate the potential influence of a prime-biased sequencing protocol on the DTU detection ability.
- added Vignettes for a Smart-seq2 single-cell data set from Wuidart et al.
- Vignettes: added sections showcasing DGE calling and priming bias detection probability calculation.
- new Dependency: `DESeq2`
- new Suggests: `glmGamPoi`, `apeglm`

# DTUrtle 0.7.4

## Changes

- `plot_transcripts_view()`: added `tested_transcripts_only` parameter, to allow better control which transcripts of a gene should be displayed. Also allows to create plot for genes which have been excluded from the analysis.
- `plot_transcripts_view()`: changed default value of `reduce_introns_fill` to ‘white’ to get visually more appealing plots by default.

# DTUrtle 0.7.3

## Changes

- readded “GenomicFeatures” as dependency - eases installation.
- measure and show computation time in vignettes.
- extended vignettes.
- extended README.
- `plot_proportion_barplot()`: define data and mapping already in general ggplot function, to ease editability.
- `plot_proportion_barplot()`: added global ‘text_size’ parameter.
- `plot_dimensional_reduction()`: added ‘plot_scale’ parameter, allowing for free x- or y-axis of facets, or both.
- `plot_dimensional_reduction()`: added global ‘text_size’ parameter.
- `plot_transcripts_view()`: added ‘arrow_start’ parameter, to allow adjustment of the transcript annotation start position.
- `plot_transcripts_view()`: changed default parameters and resolution, to get visually more appealing high quality plots.
- `import_gtf()`: generalized function and added parameter for returned feature type and return format. Now can create fitting `plot_transcripts_view()` GTF input.
- `run_drimseq()`: added `susbet_feature` and `subset_sample` parameters, replacing `subset_counts`. Now samples and features can be excluded from analysis on the fly.
- `run_drimseq()`: added `add_pseudocount` parameter, to enable comparisons of features with zero expression in one comparison group.
- `run_drimseq()`: added `filter_only` parameter, to return (sparse) count matrix after group-based filtering.
- `combine_to_matrix()`: added ability to infer Seurat cellname extension.
- removed dependency of ‘stringi’.
- added ‘sparseDRIMSeq’ to depending packages, to get rid of sometimes not-occurring package load.
- fixed some smaller bugs.

# DTUrtle 0.7.1

## Changes

- add new vignette for Tabula Muris (Mouse) data set.
- `combine_to_matrix()`: added `cell_extension_side` parameter to choose label append or prepend.
- `plot_dimensional_reduction()`: added functionality to plot in dimensional reduction space.
- `plot_transcripts_view()`: safer and more specific IdeoGram track generation.
- `plot_transcripts_view()`: improved handling of non-UCSC chromosome identifiers.
- `run_drimseq()`: added check for matching names of counts and tx2gene.
- `run_drimseq()`: added `subset_counts` parameter - ability to force subset the count matrix to matching tx2gene features only.
- `plot_dtu_table()`: disable warning for server side rendering.
- `plot_proportion_pheatmap()`: plots names are now run through `make.names()`, as all other plots.
- `create_dtu_table()`: changed default column names and added description of column meaning.
- extended checks for provided file paths.
- safer BiocParallel starting and stopping.
- made whole package documentation searchable via docsearch.
- README: fixed typo and added link to vignettes.
- set GenomeInfoDb as standard Imports.
- minor improvements.

# DTUrtle 0.2.6

## Changes

- add `add_to_table` parameter to plotting functions, to add plot savepaths directly to `dtu_table`.
- `run_drimseq()`: added description of predefined filter strategies.
- `run_drimseq()`: added check if two sample groups are left after excluding unused samples.
- minor update of function documentation.
- `plot_dtu_table()`: add `min_page_length` parameter.
- `plot_dtu_table()`: slightly change icon and heading alignment.
- added conditional vignette evaluation.
- added `knitr` in Suggests for vignette building.

# DTUrtle 0.2.5

## Changes

- initial first version.