Merge pull request loosolab#22 from HendrikSchultheis/cran

Cran

.Rbuildignore

@@ -2,3 +2,4 @@
 ^\.Rproj\.user$
 ^\.buildkite.*
 ^revdep$
+^cran-comments.md$

DESCRIPTION

@@ -6,10 +6,10 @@ Authors@R: c(
     person("Hendrik", "Schultheis", email = "hendrik.schultheis@mpi-bn.mpg.de", role = c("aut", "cre")),
     person("Jens", "Preussner", email = "jens.preussner@mpi-bn.mpg.de", role = "aut"),
     person("Looso", "Mario", email = "mario.looso@mpi-bn.mpg.de", role = "aut"))
-Description: This package provides modules for web-based tools that use plot based strategies to visualize and analyze multi-omics data.
-    'wilson' utilizes the 'shiny' and 'plotly' frameworks to provide a user friendly dashboard for interactive plotting.
-URL: https://github.molgen.mpg.de/loosolab/wilson
-BugReports: https://github.molgen.mpg.de/loosolab/wilson/issues
+Description: Tool-set of modules for creating web-based applications that use plot based strategies to visualize and analyze multi-omics data.
+    This package utilizes the 'shiny' and 'plotly' frameworks to provide a user friendly dashboard for interactive plotting.
+URL: https://github.molgen.mpg.de/loosolab/wilson/
+BugReports: https://github.molgen.mpg.de/loosolab/wilson/issues/
 License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
@@ -47,4 +47,7 @@ Imports: shiny,
     methods,
     R6
 RoxygenNote: 6.0.1
-biocViews:
+biocViews: 
+Suggests: knitr,
+    rmarkdown
+VignetteBuilder: knitr

NEWS.md

@@ -0,0 +1,23 @@
+# wilson 2.0.0 
+## Features
+- clarion class:
+  - easier data-format validation by providing several checks
+  - simplified module usage (only forward clarion object) for top-level modules (e.g. filter & plot)
+  - provide functions for frequent tasks (e.g. get_name, is_delimited, etc.)
+
+- geneView: 
+  - group columns by one or more factors
+
+- pca:
+  - color & shape grouping by selected factor(s)
+
+- scatterPlot:
+  - add name to hovertext if available (only interactive)
+
+## Misc
+- improved notifications (closable, more)
+- overall code quality improvements via usage of packages goodpractice and lintr
+- removed deprecated colorPicker
+
+# wilson 1.0.0
+first public release

R/release_questions.R

@@ -0,0 +1,14 @@
+#' Defines additional questions asked before CRAN submission.
+#' DO NOT EXPORT!
+release_questions <- function() {
+  c(
+    "Updated NEWS.md?",
+    "Updated README.md?",
+    "Re-run reverse dependencies?",
+    "Everything checked?",
+    "Abide good practices?",
+    "Updated cran-comments.md?",
+    "Updated vignettes?",
+    "Version upped?"
+  )
+}

README.md

@@ -1,5 +1,5 @@
 # WIlsON: Webbased Interactive Omics visualizatioN -  The R Package
-*Buildkite:* [![Build status](https://badge.buildkite.com/d79f55bb3e3cf0d70d6784feb8c6e26182d602f534e74fac4e.svg?branch=master)](https://buildkite.com/loosolab/wilson)
+*Buildkite:* ![Build status](https://badge.buildkite.com/d79f55bb3e3cf0d70d6784feb8c6e26182d602f534e74fac4e.svg?branch=master)
 
 ## Abstract
 #### Objective
@@ -12,9 +12,9 @@ The WIlsON R package employs the R Shiny and Plotly web-based frameworks using a
 The WIlsON R package includes a toolbox of R Shiny modules that can be used to construct a wide array of web-interfaces for plotting feature-based data.
 
 ## Availability
-All components of the WIlsON R package have been implemented in an integrated web application that is available for download from the Github repository [wilson-apps](https://github.molgen.mpg.de/loosolab/wilson-apps) and can be tested on our [official demonstration server](http://loosolab.mpi-bn.mpg.de/apps/wilson/).
+All components of the WIlsON R package have been implemented in an integrated web application that is available for download from the Github repository [wilson-apps](https://github.molgen.mpg.de/loosolab/wilson-apps/) and can be tested on our [official demonstration server](http://loosolab.mpi-bn.mpg.de/apps/wilson/).
 
-Usage instructions can be found in the extensive [documentation](https://github.molgen.mpg.de/loosolab/wilson-apps/wiki).
+Usage instructions can be found in the extensive [documentation](https://github.molgen.mpg.de/loosolab/wilson-apps/wiki/).
 
 Get a Docker container [here](https://hub.docker.com/r/loosolab/wilson/).
 
@@ -37,7 +37,7 @@ CLARION: generiC fiLe formAt foR quantItative cOmparsions of high throughput scr
 
 CLARION is a data format especially developed to be used with WIlsON, which relies on a tab-delimited table with a metadata header to describe the following columns. It is based on the Summarized Experiment format and supports all types of data which can be reduced to features and their annotation (e.g. genes, transcripts, proteins, probes) with assigned numerical values (e.g. count, score, log2foldchange, z-score, p-value). Most result tables derived from RNA-Seq, ChIP/ATAC-Seq, Proteomics, Microarrays, and many other analyses can thus be easily reformatted to become compatible without having to modify the code of WIlsON for each specific experiment.
 
-Please check the following link for details considering the [CLARION format](https://github.molgen.mpg.de/loosolab/wilson-apps/wiki/CLARION-Format).
+Please check the following link for details considering the [CLARION format](https://github.molgen.mpg.de/loosolab/wilson-apps/wiki/CLARION-Format/).
 
 ## How to cite
 *Schultheis H, Kuenne C, Preussner J, Wiegandt R, Fust A, Bentsen M, Looso M*. WIlsON: Webbased Interactive Omics VisualizatioN. (2018), doi: https://XY

cran-comments.md

@@ -0,0 +1,22 @@
+## Test environments
+* local windows 7 install, R 3.5.1
+* debian 9.4, R 3.4.1
+* win-builder (devel and release)
+
+## R CMD check results
+There were no ERRORs or WARNINGs.
+
+There was 1 NOTE:
+
+* New submission
+
+* Possibly mis-spelled words in DESCRIPTION:
+  Omics (3:30)
+  omics (9:126)
+
+  Both are spelled correctly. First is capital because of title case.
+
+## Downstream dependencies
+I have also run R CMD check on downstream dependencies of wilson 
+(https://github.molgen.mpg.de/loosolab/wilson/tree/master/revdep). 
+All packages that I could install passed.

revdep/README.md

@@ -4,48 +4,50 @@
 
 |setting  |value                        |
 |:--------|:----------------------------|
-|version  |R version 3.5.0 (2018-04-23) |
+|version  |R version 3.5.1 (2018-07-02) |
 |system   |x86_64, mingw32              |
 |ui       |RStudio (1.2.747)            |
 |language |(EN)                         |
 |collate  |German_Germany.1252          |
 |tz       |Europe/Berlin                |
-|date     |2018-06-29                   |
+|date     |2018-07-04                   |
 
 ## Packages
 
 |package         |*  |version |date       |source                              |
 |:---------------|:--|:-------|:----------|:-----------------------------------|
-|circlize        |   |0.4.4   |2018-06-10 |CRAN (R 3.5.0)                      |
-|colourpicker    |   |1.0     |2017-09-27 |CRAN (R 3.5.0)                      |
+|circlize        |   |0.4.4   |2018-06-10 |CRAN (R 3.5.1)                      |
+|colourpicker    |   |1.0     |2017-09-27 |CRAN (R 3.5.1)                      |
 |ComplexHeatmap  |   |1.18.1  |2018-06-19 |Bioconductor (R 3.5.0)              |
-|data.table      |   |1.11.4  |2018-05-27 |CRAN (R 3.5.0)                      |
+|data.table      |   |1.11.4  |2018-05-27 |CRAN (R 3.5.1)                      |
 |DESeq2          |   |1.20.0  |2018-05-01 |Bioconductor                        |
-|DT              |   |0.4     |2018-01-30 |CRAN (R 3.5.0)                      |
-|factoextra      |   |1.0.5   |2017-08-22 |CRAN (R 3.5.0)                      |
-|FactoMineR      |   |1.41    |2018-05-04 |CRAN (R 3.5.0)                      |
-|ggplot2         |   |2.2.1   |2016-12-30 |CRAN (R 3.5.0)                      |
-|ggrepel         |   |0.8.0   |2018-05-09 |CRAN (R 3.5.0)                      |
-|gplots          |   |3.0.1   |2016-03-30 |CRAN (R 3.5.0)                      |
-|heatmaply       |   |0.15.0  |2018-06-23 |CRAN (R 3.5.0)                      |
-|log4r           |   |0.2     |2014-09-29 |CRAN (R 3.5.0)                      |
-|openssl         |   |1.0.1   |2018-03-03 |CRAN (R 3.5.0)                      |
-|plotly          |   |4.7.1   |2017-07-29 |CRAN (R 3.5.0)                      |
-|plyr            |   |1.8.4   |2016-06-08 |CRAN (R 3.5.0)                      |
-|R6              |   |2.2.2   |2017-06-17 |CRAN (R 3.5.0)                      |
+|DT              |   |0.4     |2018-01-30 |CRAN (R 3.5.1)                      |
+|factoextra      |   |1.0.5   |2017-08-22 |CRAN (R 3.5.1)                      |
+|FactoMineR      |   |1.41    |2018-05-04 |CRAN (R 3.5.1)                      |
+|ggplot2         |   |2.2.1   |2016-12-30 |CRAN (R 3.5.1)                      |
+|ggrepel         |   |0.8.0   |2018-05-09 |CRAN (R 3.5.1)                      |
+|gplots          |   |3.0.1   |2016-03-30 |CRAN (R 3.5.1)                      |
+|heatmaply       |   |0.15.0  |2018-06-23 |CRAN (R 3.5.1)                      |
+|knitr           |   |1.20    |2018-02-20 |CRAN (R 3.5.1)                      |
+|log4r           |   |0.2     |2014-09-29 |CRAN (R 3.5.1)                      |
+|openssl         |   |1.0.1   |2018-03-03 |CRAN (R 3.5.1)                      |
+|plotly          |   |4.7.1   |2017-07-29 |CRAN (R 3.5.1)                      |
+|plyr            |   |1.8.4   |2016-06-08 |CRAN (R 3.5.1)                      |
+|R6              |   |2.2.2   |2017-06-17 |CRAN (R 3.5.1)                      |
 |RColorBrewer    |   |1.1-2   |2014-12-07 |CRAN (R 3.5.0)                      |
-|reshape         |   |0.8.7   |2017-08-06 |CRAN (R 3.5.0)                      |
-|rintrojs        |   |0.2.0   |2017-07-04 |CRAN (R 3.5.0)                      |
+|reshape         |   |0.8.7   |2017-08-06 |CRAN (R 3.5.1)                      |
+|rintrojs        |   |0.2.0   |2017-07-04 |CRAN (R 3.5.1)                      |
 |rje             |   |1.9     |2014-08-06 |CRAN (R 3.5.0)                      |
 |rjson           |   |0.2.20  |2018-06-08 |CRAN (R 3.5.0)                      |
 |RJSONIO         |   |1.3-0   |2014-07-28 |CRAN (R 3.5.0)                      |
-|scales          |   |0.5.0   |2017-08-24 |CRAN (R 3.5.0)                      |
-|shiny           |   |1.1.0   |2018-05-17 |CRAN (R 3.5.0)                      |
-|shinycssloaders |   |0.2.0   |2017-05-12 |CRAN (R 3.5.0)                      |
-|shinydashboard  |   |0.7.0   |2018-03-21 |CRAN (R 3.5.0)                      |
-|shinyjs         |   |1.0     |2018-01-08 |CRAN (R 3.5.0)                      |
-|viridis         |   |0.5.1   |2018-03-29 |CRAN (R 3.5.0)                      |
-|wilson          |   |2.0.0   |2018-06-29 |local (HendrikSchultheis/wilson@NA) |
+|rmarkdown       |   |1.10    |2018-06-11 |CRAN (R 3.5.1)                      |
+|scales          |   |0.5.0   |2017-08-24 |CRAN (R 3.5.1)                      |
+|shiny           |   |1.1.0   |2018-05-17 |CRAN (R 3.5.1)                      |
+|shinycssloaders |   |0.2.0   |2017-05-12 |CRAN (R 3.5.1)                      |
+|shinydashboard  |   |0.7.0   |2018-03-21 |CRAN (R 3.5.1)                      |
+|shinyjs         |   |1.0     |2018-01-08 |CRAN (R 3.5.1)                      |
+|viridis         |   |0.5.1   |2018-03-29 |CRAN (R 3.5.1)                      |
+|wilson          |*  |2.0.0   |2018-07-04 |local (HendrikSchultheis/wilson@NA) |
 
 # Check results
 

revdep/problems.md

@@ -4,48 +4,50 @@
 
 |setting  |value                        |
 |:--------|:----------------------------|
-|version  |R version 3.5.0 (2018-04-23) |
+|version  |R version 3.5.1 (2018-07-02) |
 |system   |x86_64, mingw32              |
 |ui       |RStudio (1.2.747)            |
 |language |(EN)                         |
 |collate  |German_Germany.1252          |
 |tz       |Europe/Berlin                |
-|date     |2018-06-29                   |
+|date     |2018-07-04                   |
 
 ## Packages
 
 |package         |*  |version |date       |source                              |
 |:---------------|:--|:-------|:----------|:-----------------------------------|
-|circlize        |   |0.4.4   |2018-06-10 |CRAN (R 3.5.0)                      |
-|colourpicker    |   |1.0     |2017-09-27 |CRAN (R 3.5.0)                      |
+|circlize        |   |0.4.4   |2018-06-10 |CRAN (R 3.5.1)                      |
+|colourpicker    |   |1.0     |2017-09-27 |CRAN (R 3.5.1)                      |
 |ComplexHeatmap  |   |1.18.1  |2018-06-19 |Bioconductor (R 3.5.0)              |
-|data.table      |   |1.11.4  |2018-05-27 |CRAN (R 3.5.0)                      |
+|data.table      |   |1.11.4  |2018-05-27 |CRAN (R 3.5.1)                      |
 |DESeq2          |   |1.20.0  |2018-05-01 |Bioconductor                        |
-|DT              |   |0.4     |2018-01-30 |CRAN (R 3.5.0)                      |
-|factoextra      |   |1.0.5   |2017-08-22 |CRAN (R 3.5.0)                      |
-|FactoMineR      |   |1.41    |2018-05-04 |CRAN (R 3.5.0)                      |
-|ggplot2         |   |2.2.1   |2016-12-30 |CRAN (R 3.5.0)                      |
-|ggrepel         |   |0.8.0   |2018-05-09 |CRAN (R 3.5.0)                      |
-|gplots          |   |3.0.1   |2016-03-30 |CRAN (R 3.5.0)                      |
-|heatmaply       |   |0.15.0  |2018-06-23 |CRAN (R 3.5.0)                      |
-|log4r           |   |0.2     |2014-09-29 |CRAN (R 3.5.0)                      |
-|openssl         |   |1.0.1   |2018-03-03 |CRAN (R 3.5.0)                      |
-|plotly          |   |4.7.1   |2017-07-29 |CRAN (R 3.5.0)                      |
-|plyr            |   |1.8.4   |2016-06-08 |CRAN (R 3.5.0)                      |
-|R6              |   |2.2.2   |2017-06-17 |CRAN (R 3.5.0)                      |
+|DT              |   |0.4     |2018-01-30 |CRAN (R 3.5.1)                      |
+|factoextra      |   |1.0.5   |2017-08-22 |CRAN (R 3.5.1)                      |
+|FactoMineR      |   |1.41    |2018-05-04 |CRAN (R 3.5.1)                      |
+|ggplot2         |   |2.2.1   |2016-12-30 |CRAN (R 3.5.1)                      |
+|ggrepel         |   |0.8.0   |2018-05-09 |CRAN (R 3.5.1)                      |
+|gplots          |   |3.0.1   |2016-03-30 |CRAN (R 3.5.1)                      |
+|heatmaply       |   |0.15.0  |2018-06-23 |CRAN (R 3.5.1)                      |
+|knitr           |   |1.20    |2018-02-20 |CRAN (R 3.5.1)                      |
+|log4r           |   |0.2     |2014-09-29 |CRAN (R 3.5.1)                      |
+|openssl         |   |1.0.1   |2018-03-03 |CRAN (R 3.5.1)                      |
+|plotly          |   |4.7.1   |2017-07-29 |CRAN (R 3.5.1)                      |
+|plyr            |   |1.8.4   |2016-06-08 |CRAN (R 3.5.1)                      |
+|R6              |   |2.2.2   |2017-06-17 |CRAN (R 3.5.1)                      |
 |RColorBrewer    |   |1.1-2   |2014-12-07 |CRAN (R 3.5.0)                      |
-|reshape         |   |0.8.7   |2017-08-06 |CRAN (R 3.5.0)                      |
-|rintrojs        |   |0.2.0   |2017-07-04 |CRAN (R 3.5.0)                      |
+|reshape         |   |0.8.7   |2017-08-06 |CRAN (R 3.5.1)                      |
+|rintrojs        |   |0.2.0   |2017-07-04 |CRAN (R 3.5.1)                      |
 |rje             |   |1.9     |2014-08-06 |CRAN (R 3.5.0)                      |
 |rjson           |   |0.2.20  |2018-06-08 |CRAN (R 3.5.0)                      |
 |RJSONIO         |   |1.3-0   |2014-07-28 |CRAN (R 3.5.0)                      |
-|scales          |   |0.5.0   |2017-08-24 |CRAN (R 3.5.0)                      |
-|shiny           |   |1.1.0   |2018-05-17 |CRAN (R 3.5.0)                      |
-|shinycssloaders |   |0.2.0   |2017-05-12 |CRAN (R 3.5.0)                      |
-|shinydashboard  |   |0.7.0   |2018-03-21 |CRAN (R 3.5.0)                      |
-|shinyjs         |   |1.0     |2018-01-08 |CRAN (R 3.5.0)                      |
-|viridis         |   |0.5.1   |2018-03-29 |CRAN (R 3.5.0)                      |
-|wilson          |   |2.0.0   |2018-06-29 |local (HendrikSchultheis/wilson@NA) |
+|rmarkdown       |   |1.10    |2018-06-11 |CRAN (R 3.5.1)                      |
+|scales          |   |0.5.0   |2017-08-24 |CRAN (R 3.5.1)                      |
+|shiny           |   |1.1.0   |2018-05-17 |CRAN (R 3.5.1)                      |
+|shinycssloaders |   |0.2.0   |2017-05-12 |CRAN (R 3.5.1)                      |
+|shinydashboard  |   |0.7.0   |2018-03-21 |CRAN (R 3.5.1)                      |
+|shinyjs         |   |1.0     |2018-01-08 |CRAN (R 3.5.1)                      |
+|viridis         |   |0.5.1   |2018-03-29 |CRAN (R 3.5.1)                      |
+|wilson          |*  |2.0.0   |2018-07-04 |local (HendrikSchultheis/wilson@NA) |
 
 # Check results