From 04fc2b11530bbe72a0a41f9f0e95b392e16d2812 Mon Sep 17 00:00:00 2001 From: Schultheis Date: Tue, 3 Jul 2018 08:54:06 +0200 Subject: [PATCH 1/9] check --as-cran --- wilson.Rproj | 1 + 1 file changed, 1 insertion(+) diff --git a/wilson.Rproj b/wilson.Rproj index 49f2092..6291372 100644 --- a/wilson.Rproj +++ b/wilson.Rproj @@ -17,3 +17,4 @@ StripTrailingWhitespace: Yes BuildType: Package PackageUseDevtools: Yes PackageInstallArgs: --no-multiarch --with-keep.source +PackageCheckArgs: --as-cran From 62ff58f92a8efedb0b3b71e39a60af87b7981854 Mon Sep 17 00:00:00 2001 From: Schultheis Date: Wed, 4 Jul 2018 10:52:40 +0200 Subject: [PATCH 2/9] introduction vignette; added tralling / to url if needed (only directories) --- DESCRIPTION | 9 +++-- README.md | 8 ++--- vignettes/intro.Rmd | 87 +++++++++++++++++++++++++++++++++++++++++++++ 3 files changed, 97 insertions(+), 7 deletions(-) create mode 100644 vignettes/intro.Rmd diff --git a/DESCRIPTION b/DESCRIPTION index 74bdc07..d802e0c 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -8,8 +8,8 @@ Authors@R: c( 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 +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 diff --git a/README.md b/README.md index 8555793..72c98fe 100644 --- a/README.md +++ b/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)](https://buildkite.com/loosolab/wilson/) ## 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 diff --git a/vignettes/intro.Rmd b/vignettes/intro.Rmd new file mode 100644 index 0000000..d9c145d --- /dev/null +++ b/vignettes/intro.Rmd @@ -0,0 +1,87 @@ +--- +title: "Introduction" +author: "Hendrik Schultheis" +date: "`r Sys.Date()`" +output: rmarkdown::html_vignette +vignette: > + %\VignetteIndexEntry{Vignette Title} + %\VignetteEngine{knitr::rmarkdown} + %\VignetteEncoding{UTF-8} +--- + +```{r setup, include = FALSE} +knitr::opts_chunk$set( + collapse = TRUE, + comment = "#>" +) +``` + +This vignette describes the intended workflow and usage of the wilson package for building an application and provides a simple example. + +**Prerequisites:** + +* be familiar with the basic structure of a [shiny-app](https://shiny.rstudio.com/articles/basics.html) and [shinydashboard](https://rstudio.github.io/shinydashboard/get_started.html) +* know how to use [shiny-modules](https://shiny.rstudio.com/articles/modules.html#using-modules) +* have a sufficient dataset in clarion-format + * either by [converting](https://github.molgen.mpg.de/loosolab/wilson-apps/wiki/CLARION-Format/) your own data + * or downloading from [here](https://github.molgen.mpg.de/loosolab/wilson-apps/tree/master/wilson-basic/data/) + +## Workflow + +The workflow of a wilson-application can roughly be divided into three basic steps: + +1. load data +2. filter data +3. visualize data + +But depending on the actual implementation neither the order nor the number of steps are set. Resulting in enhanced usability as for example the filter can be changed at any given time. + +## Example + +In this example we will create a wilson-application with a static dataset, a single visualization method and a preceding filter, seperated into a *Filter* and a *Visualization* tab. + +So to start we first import the needed packages and afterwards define the application interface: +``` +library(shiny) +library(shinydashboard) +library(wilson) + +# Define UI for application +ui <- dashboardPage( + header = dashboardHeader(disable = TRUE), + sidebar = dashboardSidebar(disable = TRUE), + body = dashboardBody( + tags$style(type = "text/css", "body {padding-top: 50px;}"), + navbarPage( + title = "wilson example", + position = "fixed-top", + tabPanel(title = "Filter", + # Load filter UI + featureSelectorUI(id = "filter")), + tabPanel(title = "Visualization", + # Load scatterplot UI + scatterPlotUI(id = "scatter")) + ))) +``` +This code creates an UI with two tabs. The first tab with the title *Filter* contains the filter UI called with `featureSelectorUI()` whereas the UI needed for a scatterplot called with `scatterPlotUI()` is enclosed by the second tab (*Visualization*). + +Second the server function needs to be as follows: +``` +# Define server logic required for filtering and plotting +server <- function(input, output, session) { + # load/ parse data + # change this path to match your file location + data <- parser("../wilson-apps/wilson-basic/data/A_RNAseq_Zhang_2015.se") + + # Load filter server logic + filtered_data <- callModule(module = featureSelector, id = "filter", clarion = data) + # Load scatterplot server logic + callModule(module = scatterPlot, id = "scatter", clarion = reactive(filtered_data()$object)) +} + +# Run the application +shinyApp(ui = ui, server = server) +``` +The server is what reacts to user interaction whithin the interface. Once started it will first parse the given [clarion](https://github.molgen.mpg.de/loosolab/wilson-apps/wiki/CLARION-Format/) file into a clarion object, performing validation steps in the process. Next the server parts of the respecting [modules](https://shiny.rstudio.com/articles/modules.html) defined in the UI (notice the matching ids) are loaded. Whereas the filter module bluntly accepts the data object with `clarion = data` the plot module receives its data via `clarion = reactive(filtered_data()$object)`. Wrapping in `reactive()` is due to the fact, that the filtered data object returned from the filter module is in a reactive context which essentially means shiny 'knows' when this variable changes. Read more about shiny's reactivity system [here](https://shiny.rstudio.com/articles/reactivity-overview.html). + +For a more advanced example of a wilson-application see the [wilson-basic app](https://github.molgen.mpg.de/loosolab/wilson-apps/blob/master/wilson-basic/app.R) in our [wilson-apps](https://github.molgen.mpg.de/loosolab/wilson-apps/) repository. From 70b400592459697cafa18a3f369fbde70535caeb Mon Sep 17 00:00:00 2001 From: Schultheis Date: Wed, 4 Jul 2018 15:14:54 +0200 Subject: [PATCH 3/9] updated reverse dependency check --- revdep/README.md | 54 +++++++++++++++++++++++---------------------- revdep/checks.rds | Bin 911 -> 956 bytes revdep/problems.md | 54 +++++++++++++++++++++++---------------------- 3 files changed, 56 insertions(+), 52 deletions(-) diff --git a/revdep/README.md b/revdep/README.md index 3b38cae..d73a3a5 100644 --- a/revdep/README.md +++ b/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) | # 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Date: Wed, 4 Jul 2018 15:16:32 +0200 Subject: [PATCH 4/9] deleted private url --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 72c98fe..1bd6f53 100644 --- a/README.md +++ b/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 From 44338f31f0369eeca2abb9f97a007143499f5ba6 Mon Sep 17 00:00:00 2001 From: Schultheis Date: Wed, 4 Jul 2018 15:20:24 +0200 Subject: [PATCH 5/9] rephrased description to comply with best practices --- DESCRIPTION | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index d802e0c..614d338 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -6,8 +6,8 @@ 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. +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 From 27c88645c139f7a3a74dfb91e002f6b8c4f16666 Mon Sep 17 00:00:00 2001 From: Schultheis Date: Wed, 4 Jul 2018 15:20:52 +0200 Subject: [PATCH 6/9] added NEWS.md --- NEWS.md | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 NEWS.md diff --git a/NEWS.md b/NEWS.md new file mode 100644 index 0000000..9cdcac3 --- /dev/null +++ b/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 From 552bfdf06ccfd733d4eed12f5939da947114e3a1 Mon Sep 17 00:00:00 2001 From: Schultheis Date: Wed, 4 Jul 2018 15:24:53 +0200 Subject: [PATCH 7/9] added submit comments --- .Rbuildignore | 1 + cran-comments.md | 22 ++++++++++++++++++++++ 2 files changed, 23 insertions(+) create mode 100644 cran-comments.md diff --git a/.Rbuildignore b/.Rbuildignore index d73b159..560d88c 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -2,3 +2,4 @@ ^\.Rproj\.user$ ^\.buildkite.* ^revdep$ +^cran-comments.md$ diff --git a/cran-comments.md b/cran-comments.md new file mode 100644 index 0000000..580a3bb --- /dev/null +++ b/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. From 1f52fd19749a74b82b92afef79e9106925d92d5b Mon Sep 17 00:00:00 2001 From: Schultheis Date: Wed, 4 Jul 2018 15:50:42 +0200 Subject: [PATCH 8/9] added release questions --- R/release_questions.R | 14 ++++++++++++++ man/release_questions.Rd | 13 +++++++++++++ 2 files changed, 27 insertions(+) create mode 100644 R/release_questions.R create mode 100644 man/release_questions.Rd diff --git a/R/release_questions.R b/R/release_questions.R new file mode 100644 index 0000000..25aa0e2 --- /dev/null +++ b/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?" + ) +} diff --git a/man/release_questions.Rd b/man/release_questions.Rd new file mode 100644 index 0000000..4d86795 --- /dev/null +++ b/man/release_questions.Rd @@ -0,0 +1,13 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/release_questions.R +\name{release_questions} +\alias{release_questions} +\title{Defines additional questions asked before CRAN submission. +DO NOT EXPORT!} +\usage{ +release_questions() +} +\description{ +Defines additional questions asked before CRAN submission. +DO NOT EXPORT! +} From 1ad156668edb958c63521a0b3240e316cd3f79cc Mon Sep 17 00:00:00 2001 From: Schultheis Date: Fri, 6 Jul 2018 15:45:15 +0200 Subject: [PATCH 9/9] applied suggested rephrasing --- vignettes/intro.Rmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/vignettes/intro.Rmd b/vignettes/intro.Rmd index d9c145d..9b9fc74 100644 --- a/vignettes/intro.Rmd +++ b/vignettes/intro.Rmd @@ -82,6 +82,6 @@ server <- function(input, output, session) { # Run the application shinyApp(ui = ui, server = server) ``` -The server is what reacts to user interaction whithin the interface. Once started it will first parse the given [clarion](https://github.molgen.mpg.de/loosolab/wilson-apps/wiki/CLARION-Format/) file into a clarion object, performing validation steps in the process. Next the server parts of the respecting [modules](https://shiny.rstudio.com/articles/modules.html) defined in the UI (notice the matching ids) are loaded. Whereas the filter module bluntly accepts the data object with `clarion = data` the plot module receives its data via `clarion = reactive(filtered_data()$object)`. Wrapping in `reactive()` is due to the fact, that the filtered data object returned from the filter module is in a reactive context which essentially means shiny 'knows' when this variable changes. Read more about shiny's reactivity system [here](https://shiny.rstudio.com/articles/reactivity-overview.html). +The server reacts to user interactions whith the interface. Once started it will first parse the given [clarion](https://github.molgen.mpg.de/loosolab/wilson-apps/wiki/CLARION-Format/) file into a clarion object, performing validation steps in the process. Next the server functions of the necessary [modules](https://shiny.rstudio.com/articles/modules.html) defined in the UI (notice the matching ids) are loaded. Whereas the filter module bluntly accepts the data object with `clarion = data` the plot module receives its data via `clarion = reactive(filtered_data()$object)`. Wrapping in `reactive()` is due to the fact, that the filtered data object returned from the filter module is in a reactive context which essentially means shiny 'knows' when this variable changes. Read more about shiny's reactivity system [here](https://shiny.rstudio.com/articles/reactivity-overview.html). For a more advanced example of a wilson-application see the [wilson-basic app](https://github.molgen.mpg.de/loosolab/wilson-apps/blob/master/wilson-basic/app.R) in our [wilson-apps](https://github.molgen.mpg.de/loosolab/wilson-apps/) repository.