# 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.
