From d87bb343d2a72ff59daee11e1bfa3313a7d22cb4 Mon Sep 17 00:00:00 2001 From: vertesy Date: Fri, 26 Nov 2021 11:21:03 +0100 Subject: [PATCH] readme --- README.md | 113 ++++++++++++++++++++--------------------------- Release.notes.md | 101 ++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 148 insertions(+), 66 deletions(-) create mode 100644 Release.notes.md diff --git a/README.md b/README.md index 2dad3a1..6a4a066 100644 --- a/README.md +++ b/README.md @@ -1,44 +1,37 @@ _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: -Package Reorganisation Diagram - -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). +R-package Tree -### 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`. +
## What is ***MarkdownReports***? @@ -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. +
+ ## Why did I make it & why you might like it too? @@ -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. +
+ ## Make figures quickly - The philosophy of the package is to ***type little*** (but draw and save correctly annotated figures). @@ -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) - +
## Write a report on the fly @@ -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.* +
+ ### Where does ***MarkdownReports*** stand out? - **Pure markdown output**, compatible, simple and elegant layout. @@ -125,24 +124,41 @@ 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. - -

+ ## 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") +```

@@ -150,6 +166,8 @@ Alternatively, you simply source it from the web. *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.* +
+ ## Discover 4 Yourself! - **Check out the [wiki](https://github.com/vertesy/MarkdownReports/wiki)!** @@ -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`. - - - -

+## #### Cite it via its Digital Object Identifier (DOI): diff --git a/Release.notes.md b/Release.notes.md new file mode 100644 index 0000000..8318ffe --- /dev/null +++ b/Release.notes.md @@ -0,0 +1,101 @@ + + _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: + + + +R-package Tree + + + +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: + +Package Reorganisation Diagram + +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`. + + + +

+ +####