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_cite via:_ [![DOI](https://zenodo.org/badge/20391/vertesy/MarkdownReports.svg)](https://zenodo.org/badge/latestdoi/20391/vertesy/MarkdownReports)

# MarkdownReportsType Less, Plot More.
# MarkdownReports – Type Less, Plot More.
MarkdownReports does quick, annotated, .pdf/.png exported plotting and compiles an report in markdown from those.



## News

### Version 4.3.2 is released
### Version 4.5.2

In a major work to form installable R-packages from all my function libraries, I reorganized the codebase as below:

<img width="915" alt="Package Reorganisation Diagram" src="https://user-images.githubusercontent.com/5101911/140038110-b0e843cf-10c7-45c7-87dc-0525fafb0f57.png">

MarkdownReports v4.3.2 Relies on
- [Stringendo](https://github.com/vertesy/Stringendo)
- [ReadWriter](https://github.com/vertesy/ReadWriter)
- [CodeAndRoll2](https://github.com/vertesy/CodeAndRoll2)

... and provides functions for
- [ggExpress](https://github.com/vertesy/ggExpress)
- [SeuratUtils](https://github.com/vertesy/SeuratUtils).


<img width="1005" alt="R-package Tree" src="https://user-images.githubusercontent.com/5101911/143560128-065d8a49-0283-4a3a-9448-540fa424d0ef.png">

### Version 4.1.0 is ready and installed by the default.

1. See legacy/old version at: https://github.com/vertesy/MarkdownReports.v2.9.5
2. See development version at: https://github.com/vertesy/MarkdownReportsDev

MarkdownReports depends on

### New features:
- [Stringendo](https://github.com/vertesy/Stringendo)
- [ReadWriter](https://github.com/vertesy/ReadWriter)
- [CodeAndRoll2](https://github.com/vertesy/CodeAndRoll2)
- [MarkdownHelpers](https://github.com/vertesy/MarkdownHelpers)

- **Formatted session info Sessioninfo**
- Updated dependencies
- Many functions are more stable and versatile
... and provides functions for
- [ggExpress](https://github.com/vertesy/ggExpress)
- [SeuratUtils](https://github.com/vertesy/SeuratUtils)

In case you find a bug, please report. Try the [development version](https://github.com/vertesy/MarkdownReportsDev/) or a legacy version. **Old versions** are under `MarkdownReports.LEGACY.VERSION.X.X.X`.


<br>

## What is ***MarkdownReports***?

Expand All @@ -52,6 +45,8 @@ MarkdownReports is a set of **R** functions that allows you to generate precise
- Version your findings, annotating which parameters were used to reach certain results.
- Share your report with others via email, Github or a personal website.

<br>


## Why did I make it & why you might like it too?

Expand All @@ -66,6 +61,8 @@ I often have to...

For all of the above, my solution is MarkdownReports. I think its better than other solutions I found. Many of those like to combine source code with results, and many are too complex to use. Most of people I interact with are not interested in the source code, but are very keen on seeing my results from all possible angles and are asking detailed questions about the analysis.

<br>

## Make figures quickly

- The philosophy of the package is to ***type little*** (but draw and save correctly annotated figures).
Expand All @@ -75,7 +72,7 @@ For all of the above, my solution is MarkdownReports. I think its better than ot
- All plot functions start with **w**, followed by the **base plot name**, such as `wplot()`, `wbarplot()`, `wpie()`, `wboxplot()`,but also `wvenn()`, `wvioplot_list()`,`wviostripchart_list()`.
- See more under: ***Discover 4 Yourself!*** (Below)


<br>

## Write a report on the fly

Expand All @@ -90,6 +87,8 @@ For all of the above, my solution is MarkdownReports. I think its better than ot
- *In Rmarkdown you would make a separate cleaned-up a script, that you then knit as a separate step.*
- **No hassle of** executing computation in **isolated code-blocks** (and importing all relevant variables there). *Your code is also a lot easier to follow because it is not split up in blocks.*

<br>

### Where does ***MarkdownReports*** stand out?

- **Pure markdown output**, compatible, simple and elegant layout.
Expand Down Expand Up @@ -125,31 +124,50 @@ and your report will have the summary: ***30.7 % or 614 of 2000 entries in GeneE
- It is all achieved in ~ 1600 lines of well documented code compiled into a proper R-package.
-


<br><br>

## Installation

Install directly from **GitHub** via **devtools** with one R command:
You can install all of them directly from **GitHub** via **devtools** with one R command:

```R
# install.packages("devtools"); # If you don't have it.
require("devtools")

# Install dependencies
devtools::install_github(repo = "vertesy/Stringendo", upgrade = F)
devtools::install_github(repo = "vertesy/CodeAndRoll2", upgrade = F)
devtools::install_github(repo = "vertesy/ReadWriter", upgrade = F)
devtools::install_github(repo = "vertesy/MarkdownHelpers", upgrade = F)

# Install MarkdownReports
devtools::install_github(repo = "vertesy/Markdownreports", upgrade = F)

```


# install.packages("devtools"); # If you don't have it.
require("devtools")
devtools::install_github(repo = "vertesy/MarkdownReports")

...then simply load the package:

require("MarkdownReports")
```R
require("MarkdownReports")
```

Alternatively, you simply source it from the web.
*This way function help will not work, and you will have no local copy of the code on your hard drive.*

source("https://raw.githubusercontent.com/vertesy/MarkdownReports/master/R/MarkdownReports.R")
```R
source("https://raw.githubusercontent.com/vertesy/MarkdownReports/master/R/MarkdownReports.R")
```

<br><br>

### Troubleshooting

*If you encounter a **bug**, something doesn't work or unclear, please let me know by raising an issue on [MarkdownReports](https://github.com/vertesy/MarkdownReports/issues) – Please check if it has been asked.*

<br>

## Discover 4 Yourself!

- **Check out the [wiki](https://github.com/vertesy/MarkdownReports/wiki)!**
Expand All @@ -172,44 +190,7 @@ Alternatively, you simply source it from the web.



## Older News

[3.1.1 is under legacy now]

### Version 3.1.1 is ready and installed by the default.

1. See legacy/old version at: https://github.com/vertesy/MarkdownReports.v2.9.5
2. See development version at: https://github.com/vertesy/MarkdownReportsDev


### New features"

- **Function argument names now mirror the `R base` argument names (99%).**

- Think of `xlb >>> xlab`, or `sub_ >>> sub`
- This however breaks the compatibility with earlier versions, so you might need to replace some function arguments
- **The package now can also work with png images.**

- You can save files in png, which can be displayed inside the markdown file on windows 7.

- You need to set `b.usepng=T` in `setup_MarkdownReports`: `setup_MarkdownReports(OutDir = "/Users/...blabla....", b.usepng=T)`
- The package contains multiple other bug fixes:

- Self consistency: some missing functions moved from `CodeAndRoll.R`
- Table writing functions `md.tableWriter.DF.w.dimnames()` and `md.tableWriter.VEC.w.names()`
- Enhancements:

- `filter_HP(), filter_LP(), filter_MidPass()` show histogram
- `whist()` can invite the above filter functions.
- Numerous other small fixes.



**Old version** is under `MarkdownReports.LEGACY.VERSION`.



<br/><br/>
##

#### Cite it via its Digital Object Identifier (DOI):

Expand Down
101 changes: 101 additions & 0 deletions Release.notes.md
Original file line number Diff line number Diff line change
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_cite via:_ [![DOI](https://zenodo.org/badge/20391/vertesy/MarkdownReports.svg)](https://zenodo.org/badge/latestdoi/20391/vertesy/MarkdownReports)

# News - MarkdownReports


## News

### Version 4.5.2

In a major work to form installable R-packages from all my function libraries, I reorganized the codebase as below:



<img width="1005" alt="R-package Tree" src="https://user-images.githubusercontent.com/5101911/143560128-065d8a49-0283-4a3a-9448-540fa424d0ef.png">



MarkdownReports v4.5.2 Relies on

- [Stringendo](https://github.com/vertesy/Stringendo)
- [ReadWriter](https://github.com/vertesy/ReadWriter)
- [CodeAndRoll2](https://github.com/vertesy/CodeAndRoll2)
- [MarkdownHelpers](https://github.com/vertesy/MarkdownHelpers)

... and provides functions for

- [ggExpress](https://github.com/vertesy/ggExpress)
- [SeuratUtils](https://github.com/vertesy/SeuratUtils)

### Version 4.3.2 is released

In a major work to form installable R-packages from all my function libraries, I reorganized the codebase as below:

<img width="915" alt="Package Reorganisation Diagram" src="https://user-images.githubusercontent.com/5101911/140038110-b0e843cf-10c7-45c7-87dc-0525fafb0f57.png">

MarkdownReports v4.3.2 Relies on
- [Stringendo](https://github.com/vertesy/Stringendo)
- [ReadWriter](https://github.com/vertesy/ReadWriter)
- [CodeAndRoll2](https://github.com/vertesy/CodeAndRoll2)

... and provides functions for
- [ggExpress](https://github.com/vertesy/ggExpress)
- [SeuratUtils](https://github.com/vertesy/SeuratUtils).



### Version 4.1.0 is ready and installed by the default.

1. See legacy/old version at: https://github.com/vertesy/MarkdownReports.v2.9.5
2. See development version at: https://github.com/vertesy/MarkdownReportsDev


### New features:

- **Formatted session info Sessioninfo**
- Updated dependencies
- Many functions are more stable and versatile

In case you find a bug, please report. Try the [development version](https://github.com/vertesy/MarkdownReportsDev/) or a legacy version. **Old versions** are under `MarkdownReports.LEGACY.VERSION.X.X.X`.



[3.1.1 is under legacy now]

### Version 3.1.1 is ready and installed by the default.

1. See legacy/old version at: https://github.com/vertesy/MarkdownReports.v2.9.5
2. See development version at: https://github.com/vertesy/MarkdownReportsDev


### New features

- **Function argument names now mirror the `R base` argument names (99%).**

- Think of `xlb >>> xlab`, or `sub_ >>> sub`
- This however breaks the compatibility with earlier versions, so you might need to replace some function arguments
- **The package now can also work with png images.**

- You can save files in png, which can be displayed inside the markdown file on windows 7.

- You need to set `b.usepng=T` in `setup_MarkdownReports`: `setup_MarkdownReports(OutDir = "/Users/...blabla....", b.usepng=T)`
- The package contains multiple other bug fixes:

- Self consistency: some missing functions moved from `CodeAndRoll.R`
- Table writing functions `md.tableWriter.DF.w.dimnames()` and `md.tableWriter.VEC.w.names()`
- Enhancements:

- `filter_HP(), filter_LP(), filter_MidPass()` show histogram
- `whist()` can invite the above filter functions.
- Numerous other small fixes.



**Old version** is under `MarkdownReports.LEGACY.VERSION`.



<br/><br/>

####

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