# NACHO 2.0.6

## Fixes

- In `R/qc_positive_control.R`,
  - fix: use R-squared instead of Pearson correlation coefficient. ([#48](https://github.com/mcanouil/NACHO/issues/48))

# NACHO 2.0.5

## Fixes

- In `R/autoplot.R`,
  - fix: set `height` in `ggplot2::position_jitter()` to `0` to avoid vertical dispersion points. ([#45](https://github.com/mcanouil/NACHO/issues/45))
- In `inst/app/www/about-nacho.md`,
  - fix: shiny[dot]rstudio[dot]com moved to <https://shiny.posit.co/>.

## Tests

- In `tests/testthat/test-load_rcc.R`,
  - fix: skip tests to decrease CRAN checks computation time.

**Full Changelog**: <https://github.com/mcanouil/NACHO/compare/v2.0.4...v2.0.5>

# NACHO 2.0.4

## Fixes

- In `inst/CITATION`,
  - fix: convert `citEntry` to `bibentry` from CRAN note.

**Full Changelog**: <https://github.com/mcanouil/NACHO/compare/v2.0.3...v2.0.4>

# NACHO 2.0.3

## Chores

- In `DESCRIPTION`,
  - chore: update domain name.

**Full Changelog**: <https://github.com/mcanouil/NACHO/compare/v2.0.2...v2.0.3>

# NACHO 2.0.2

## Chores

- In `DESCRIPTION`,
  - chore: update email address.
- chore: remove `ggbeeswarm`.

**Full Changelog**: <https://github.com/mcanouil/NACHO/compare/v2.0.1...v2.0.2>

# NACHO 2.0.1

## Chores

- In `DESCRIPTION`,
  - chore: update email address.

**Full Changelog**: <https://github.com/mcanouil/NACHO/compare/v2.0.0...v2.0.1>

# NACHO 2.0.0

## Major (breaking) changes

- Refactor to use `data.table` instead of `dplyr`/`tidyr`/`purrr`.

## Features

- Ensure RCC files are homogeneous in terms of versions. [#20](https://github.com/mcanouil/NACHO/issues/20)
- Allow to use vector of file paths, named or not. [#33](https://github.com/mcanouil/NACHO/issues/33)
- Allow to upload a CSV file associated with the RCC files within the `shiny` application. [#36](https://github.com/mcanouil/NACHO/issues/36)

Full Changelog: <https://github.com/mcanouil/NACHO/compare/v1.1.0...v2.0.0>

# NACHO 1.1.0

## Breaking changes

- In `DESCRIPTION`,
  - Update `ggplot2` version (>= 3.3.0).
  - Update `dplyr` version (>= 1.0.2).
- In `R/autoplot.R`,
  - Replace `ggplot2::expand_scale()` with `ggplot2::expansion()`.

## Minor improvements and fixes

- In `R/load_rcc.R`,
  - Remove deprecated `dplyr::progress_estimated()`.
- In `R/norm_glm.R`,
  - Remove deprecated `dplyr::progress_estimated()`.
- In `tests`,
  - Small tweaks.
  - Add condition when trying to download files from a GEO dataset (Fix CRAN checks).

# NACHO 1.0.2

## Minor improvements and fixes

- In `DESCRIPTION`,
  - Update URLs.
- In `R/normalise.R`,
  - Fix missing "outliers_thresholds" field after `normalise()` without removing outliers (#26).
- In `R/GSE74821.R`,
  - Now uses `data-raw` root directory.
- In `R/-`,
  - No longer generates `Rd` files for internal functions.

# NACHO 1.0.1

## Minor improvements and fixes

- Fix deprecated documentation for `R/load_rcc.R` and `R/normalise.R`.
- Use `file.path()` in examples and vignette.
- In `R/autoplot.R`, reduce alpha for ellipses.
- In `inst/app/utils.R`, set default point size (also for outliers) to `1`.
- In `R/load_rcc.R`, use `inherits()` instead of `class()`.
- Code optimisation.

# NACHO 1.0.0

## New features

- In `R/conflicts.R`,
  - conflicts are now printed when attaching `NACHO`.
  - `nacho_conflicts()` can be used to print conflicts.
- New Shiny app in `inst/app/`, (#4, #5 & #14)
  - as a regular app, to load directly RCC files individually or within zip archive.
  - within `visualise()`, to load `"nacho"` object from `load_rcc()` (previous `summarise()`)
        or from `normalise()`.
- New `deploy()` (`R/deploy.R`) function to easily deploy (copy) the shiny app.
- New raw RCC files (multiplexed) available in `inst/extdata/`.
- New vignette `NACHO-analysis`, which describe how to use `limma` or other model after using --NACHO--.
- In `DESCRIPTION`,
  - Order packages in alphabetical order.
  - Add packages' version.

## Breaking changes

- `summarise()` and `summarize()` have been deprecated and replaced with `load_rcc()`. (#12 & #15)
- Counts matrices (`raw_counts` and `normalised_counts`) are no longer (directly) available,
  -i.e.-, counts are available in a long format within the `nacho` slot of a nacho object.
- `visualise()`, now uses a new shiny app (`inst/app/`).

## Minor improvements and fixes

- In `R/visualise.R`, `R/render.R`, `print()`, `R/load_rcc.R` and `R/normalise.R`,
  - replace function to check for outliers, now uses `check_outliers()`.
- In `R/visualise.R`, replace datatable (render and output) with classical table. (#13)
- In `R/autoplot.R`,
  - add `show_outliers` to show outliers differently on plots (-i.e.-, in red).
  - add `outliers_factor` to highligth outliers with different point size.
  - add `outliers_labels` to print labels on top of outliers.
  - now uses tidyeval via import.
  - remove plexset ID (`_S-`) to remove duplicated QC metrics.
- In `R/print.R`, now print a table with outliers if any (with `echo = TRUE`).
- In `R/GSE74821.R`, dataset is up to date according to NACHO functions.

# NACHO 0.6.1

## Minor improvements and fixes

- In `DESCRIPTION`, add `"SystemRequirements: pandoc (>= 1.12.3) - http://pandoc.org, pandoc-citeproc"`.
- In `R/render.R`,
  - explicit import for `opts_chunk::knitr` in roxygen documentation.
  - explicit import for `sessioninfo::session_info` in roxygen documentation.
- In `tests/testthat/test-render.R`, now checks if pandoc is available.
- In `tests/testthat/test-summarise.R`, fix tests when connection to GEO is alternatively up/down between two tests.

# NACHO 0.6.0

## Citation

- Add citation (#8).

## New features

- `autoplot()` allows to plot a chosen QC plot available in the shiny app (`visualise()`) and/or
  in the HTML report (`render()`).
- `print()` allows to print the structure or to print text and figures formatted using markdown
  (mainly to be used in a Rmakrdown chunk).
- `render()` render figures from `visualise()` in a HTML friendly output.

## Minor improvements and fixes

- In `R/read_rcc.R`, `R/summarise.R`,
  - fix issue (#1) when PlexSet RCC files could not be read.
  - update code to use `tidyr` 1.0.0 (#9).
- In `R/summarise.R`,
  - object returned is of S3 class "nacho" for ease of use of `autoplot()`.
  - update code to use `tidyr` 1.0.0 (#9).
- In `R/normalise.R`,
  - object returned is of S3 class "nacho" for ease of use of `autoplot()`.
  - fix missing `outliers_thresholds` component in returned object.
- In `R/visualise.R`,
  - minor code changes.
  - return `app` object in non-interactive session.
- In `vignettes/NACHO.Rmd`,
  - fix several typos.
  - add sections for `autoplot()`, `print()` and `render()` (#7).
  - fix chunk output (-i.e.-, remove default `results = "asis"`).
  - fix `normalise()` call with custom housekeeping genes (-i.e.-, set `housekeeping_predict = FALSE`) (#10).

# NACHO 0.5.6

## Minor improvements and fixes

- In `tests/testthat/test-summarise.R`, add condition to handle when `GEOQuery` is down and cannot retrieve online data.
- In `vignettes/NACHO.Rmd`, add condition to handle when `GEOQuery` is down and cannot retrieve online data.

# NACHO 0.5.5

## Minor improvements and fixes

- In `R/summarise.R`, put example in `if (interactive()) {...}` instead of `\dontrun{...}`.
- In `R/normalise.R`, put example in `if (interactive()) {...}` instead of `\dontrun{...}`.
- In `R/visualise.R`, put example in `if (interactive()) {...}` instead of `\dontrun{...}`.
- In `DESCRIPTION` and `README`, description updated for CRAN, by adding "messenger-RNA/micro-RNA".

# NACHO 0.5.4

## Minor improvements and fixes

- In `R/normalise.R`, add short running example for `normalise()`.
- In `R/visualise.R`, add short running example for `visualise()`.
- In `DESCRIPTION`, description updated for CRAN, by removing some capital letters
 and put --NACHO-- between single quotes.

# NACHO 0.5.3

## Minor improvements and fixes

- Bold letters for --NACHO-- in title.
- In `DESCRIPTION`, title and description updated for CRAN.
- Add NanoString reference in `DESCRIPTION` and vignette

# NACHO 0.5.2

## Minor improvements and fixes

- In `DESCRIPTION`, title and description updated for CRAN.

# NACHO 0.5.1

## Minor improvements and fixes

- Vignette uses bib file for references.
- Update URL in DESCRIPTION.

# NACHO 0.5.0

## New features

- `summarise()` imports and pre-process RCC files.
- `normalise()` allows to change settings used in `summarise()` and exclude outliers.
- `visualise()` allows customisation of the quality thresholds.
- Minor changes

## Minor improvements and fixes

- Add a README.
- Add logo.
- In `summarise()`, `ssheet_csv` can take a data.frame or a csv file.
- Change in package title with capital letters corresponding to NACHO.
- Add tests using testthat.

# NACHO 0.4.0

- Fix major errors, bad behaviour and typos.

# NACHO 0.3.1

- Add and fill roxygen documentation.

# NACHO 0.3.0

- Code optimisation in `normalise()` (and internal functions).
- `visualise()` replaces the Shiny app.

# NACHO 0.2.2

- Remove S4 class => Back to list object.

# NACHO 0.2.1

- Rewrite GEO dataset.

# NACHO 0.2.0

- Complete rewrite of `summarise()` and `normalise()` (and all internal functions).
- Add S4 class object.

# NACHO 0.1.0

- First version.
