Merge pull request #3 from royfrancis/v2.1.1

Adding changes for v2.1.1

.Rbuildignore

@@ -0,0 +1,15 @@
+^.*\.Rproj$
+^\.Rproj\.user$
+^\.Rhistory
+^\.Rdata
+pkgdown/
+_pkgdown.yml
+docs/
+index.md
+NEWS.md
+^\.github/
+^\.git/
+vignettes/
+vignettes/*
+^\.\.Rcheck/
+Dockerfile

.github/workflows/build.yml

@@ -1,7 +1,5 @@
 ## GITHUB ACTION FOR R PACKAGE
 ## Build, check
-## Required secrets
-## TOKEN
 
 name: build
 on:
@@ -16,7 +14,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        r: [3.5.3,3.6.3,4.0.0]
+        r: [3.6,4.0]
     steps:
       - uses: actions/checkout@v1
       - uses: r-lib/actions/setup-r@master
@@ -42,6 +40,7 @@ jobs:
         if: steps.cache-r-packages.outputs.cache-hit != 'true'
         run: |
           Rscript -e "install.packages(c('remotes','rcmdcheck'))"
+          Rscript -e "remotes::install_github('royfrancis/pophelper',dependencies=TRUE)"
           Rscript -e "remotes::install_deps(pkgdir='.',dependencies=TRUE,repos='https://cran.rstudio.com/')"
       - name: RMD check and install package
         run: |
@@ -53,7 +52,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        r: [3.5.3,3.6.3,4.0.0]
+        r: [3.6,4.0]
     steps:
       - uses: actions/checkout@v1
       - uses: r-lib/actions/setup-r@master
@@ -71,6 +70,7 @@ jobs:
         if: steps.cache-r-packages.outputs.cache-hit != 'true'
         run: |
           Rscript -e "install.packages(c('remotes','rcmdcheck','stringi'),lib='C:/R/library')"
+          Rscript -e "remotes::install_github('royfrancis/pophelper',dependencies=TRUE)"
           Rscript -e "remotes::install_deps(pkgdir='.',dependencies=TRUE,repos='https://cran.rstudio.com/',lib='C:/R/library')"
           Rscript -e "(print(.libPaths()))"
       - name: RMD check and install package

.github/workflows/docker.yml

@@ -6,12 +6,12 @@ on:
 
 jobs:
   push_to_registry:
-    name: Push docker image to dockerhub
+    name: Build/Push docker image to dockerhub
     runs-on: ubuntu-latest
     steps:
-      - name: check out the repo
+      - name: Check out the repo
         uses: actions/checkout@v2
-      - name: push to dockerhub
+      - name: Build and push to dockerhub
         uses: docker/build-push-action@v1
         with:
           username: ${{ secrets.DOCKER_USERNAME }}

.gitignore

@@ -0,0 +1 @@
+inst/doc

DESCRIPTION

@@ -1,43 +1,36 @@
 Package: pophelperShiny
 Type: Package
 Title: Interactive shiny GUI around pophelper R package
-Version: 2.1.0
-Date: 2019-08-15
+Version: 2.1.1
+Date: 2020-12-28
 Author: Roy Mathew Francis
 Authors@R: person("Roy", "Francis", email = "[email protected]",role = c("aut", "cre"))
 Maintainer: Roy Mathew Francis <[email protected]>
 Description: Interactive interface to pophelper using shiny web framework.
 URL: https://github.com/royfrancis/pophelperShiny
 Depends:
-    R(>= 3.5.0),
-    ggplot2,
-    highcharter,
-    magrittr,
-    pophelper(>= 2.3.0),
-    shiny
+    R(>= 3.6)
 Imports:
     colourpicker,
     DT,
+    ggplot2,
     gridExtra,
+    highcharter,
     htmlwidgets,
     magrittr,
-    markdown,   
+    pophelper(>= 2.3.1),
     RColorBrewer,
+    shiny,
     shinyAce,
     shinyBS,
     shinythemes,
     shinyWidgets,
     tidyr,
     viridisLite,
     writexl
-Suggests:
-    bookdown,
-    captioner,
-    ggpubr,
-    knitr,
-    markdown
+Remotes:
+    royfrancis/pophelper
 License: GPL-3
 Encoding: UTF-8
 BugReports: https://github.com/royfrancis/pophelperShiny/issues
-VignetteBuilder: knitr
-RoxygenNote: 6.1.1
+RoxygenNote: 7.1.1

Dockerfile

@@ -0,0 +1,40 @@
+# DOCKER FILE FOR POPHELPERSHINY
+# 2021 Roy Francis
+
+FROM rocker/shiny:4.0.3
+LABEL Description="Docker image for R package pophelperShiny"
+LABEL Maintainer="[email protected]"
+
+RUN apt-get update -y \
+  && apt-get install --no-install-recommends -y \
+  libfreetype6-dev \
+  libcurl4-openssl-dev \
+  libssl-dev \
+  libudunits2-dev \
+  libxml2-dev \
+  libgeos-dev \
+  libfontconfig1-dev \
+  gdal-bin \
+  libgdal-dev \
+  libcairo2-dev \
+  libxt-dev \
+  libnlopt-dev \
+  mesa-common-dev \
+  libglu1-mesa-dev \
+  libx11-dev \
+  && rm -rf /var/lib/apt/lists/*
+
+# install r packages
+RUN Rscript -e 'install.packages(c("ggplot2","gridExtra","label.switching","tidyr","remotes","colourpicker","DT","highcharter","htmlwidgets","magrittr","markdown","RColorBrewer","shiny","shinyAce","shinyBS","shinythemes","shinyWidgets","viridisLite","writexl"),repos = "http://cran.us.r-project.org");'
+
+# install pophelper package from github
+RUN Rscript -e 'remotes::install_github("royfrancis/pophelper")'
+RUN Rscript -e 'remotes::install_github("royfrancis/pophelperShiny")'
+
+RUN cd /srv/shiny-server && \
+    ln -s /usr/local/lib/R/site-library/pophelperShiny/app && \
+    sudo chown -R shiny:shiny /srv/shiny-server/app
+
+EXPOSE 3838
+
+CMD ["R", "-e", "shiny::runApp('/srv/shiny-server/app/', host = '0.0.0.0', port = 8787)"]

NAMESPACE

@@ -1,13 +1,83 @@
 # Generated by roxygen2: do not edit by hand
 
 export(runPophelper)
+import(ggplot2)
+import(highcharter)
+import(magrittr)
+import(pophelper)
 importFrom(DT,dataTableOutput)
 importFrom(DT,renderDataTable)
 importFrom(RColorBrewer,brewer.pal)
 importFrom(colourpicker,colourInput)
 importFrom(colourpicker,updateColourInput)
 importFrom(gridExtra,grid.arrange)
 importFrom(htmlwidgets,JS)
+importFrom(shiny,HTML)
+importFrom(shiny,Progress)
+importFrom(shiny,actionButton)
+importFrom(shiny,br)
+importFrom(shiny,checkboxInput)
+importFrom(shiny,column)
+importFrom(shiny,conditionalPanel)
+importFrom(shiny,div)
+importFrom(shiny,downloadButton)
+importFrom(shiny,downloadHandler)
+importFrom(shiny,eventReactive)
+importFrom(shiny,fileInput)
+importFrom(shiny,fluidPage)
+importFrom(shiny,fluidRow)
+importFrom(shiny,h1)
+importFrom(shiny,h2)
+importFrom(shiny,h3)
+importFrom(shiny,h4)
+importFrom(shiny,h5)
+importFrom(shiny,h6)
+importFrom(shiny,helpText)
+importFrom(shiny,hr)
+importFrom(shiny,htmlOutput)
+importFrom(shiny,imageOutput)
+importFrom(shiny,incProgress)
+importFrom(shiny,inputPanel)
+importFrom(shiny,isolate)
+importFrom(shiny,mainPanel)
+importFrom(shiny,numericInput)
+importFrom(shiny,observe)
+importFrom(shiny,observeEvent)
+importFrom(shiny,reactive)
+importFrom(shiny,reactiveValues)
+importFrom(shiny,renderImage)
+importFrom(shiny,renderPlot)
+importFrom(shiny,renderPrint)
+importFrom(shiny,renderTable)
+importFrom(shiny,renderText)
+importFrom(shiny,renderUI)
+importFrom(shiny,req)
+importFrom(shiny,runApp)
+importFrom(shiny,selectInput)
+importFrom(shiny,selectizeInput)
+importFrom(shiny,setProgress)
+importFrom(shiny,sidebarLayout)
+importFrom(shiny,sidebarPanel)
+importFrom(shiny,sliderInput)
+importFrom(shiny,submitButton)
+importFrom(shiny,tabPanel)
+importFrom(shiny,tabsetPanel)
+importFrom(shiny,tagList)
+importFrom(shiny,tags)
+importFrom(shiny,textInput)
+importFrom(shiny,titlePanel)
+importFrom(shiny,uiOutput)
+importFrom(shiny,updateActionButton)
+importFrom(shiny,updateCheckboxInput)
+importFrom(shiny,updateNumericInput)
+importFrom(shiny,updateSelectInput)
+importFrom(shiny,updateSelectizeInput)
+importFrom(shiny,updateSliderInput)
+importFrom(shiny,updateTextInput)
+importFrom(shiny,validate)
+importFrom(shiny,verbatimTextOutput)
+importFrom(shiny,wellPanel)
+importFrom(shiny,withProgress)
 importFrom(shinyAce,aceEditor)
 importFrom(shinyBS,bsTooltip)
 importFrom(shinyWidgets,pickerInput)

NEWS

@@ -1,3 +1,11 @@
+pophelperShiny 2.1.1
+====================
+28-Dec-2020
+* Based on pophelper_v2.3.1
+* Error bars in first plot of Evanno method showed max/min rather than SD. Fixed to show SD.
+* Legend is now sorted numerically
+* Better CRAN compatibility
+
 pophelperShiny 2.1.0
 ====================
 * 15-Aug-2019

inst/app/versions.md → NEWS.md

@@ -1,30 +1,32 @@
-#### v2.1.0
+# pophelperShiny 2.1.1
+
+* 28-Dec-2020
+* Based on pophelper_v2.3.1
+* Error bars in first plot of Evanno method showed max/min rather than SD. Fixed to show SD.
+* Legend is now sorted numerically
+* Better CRAN compatibility
+
+# pophelperShiny 2.1.0
 
 * 15-Aug-2019
 * R dependency set to >=3.5.0
 * Based on pophelper_v2.3.0
 * Added cluster colour palette picker with palette image
 * 'Colorbrewer' option removed and added to regular colours
 * Added R package **shinyWidgets**
-* Runs selection for plots do not maintain selection order
 * Runs selection options using datatable widget or picker widget
 * Excel dependency changed from **xlsx** to **writexl**
 * Dependency on CLUMPP executable removed
 * Align function added to align clusters within and across K
 * Temporary files and plots written in temporary directory
 
-#### v2.0.1
+# pophelperShiny 2.0.1
 
 * 17-Sep-2018
 * Removed dependency on **fields** package
 * Temporary directory is set to OS default
 
-#### v2.0.0
+# pophelperShiny 2.0.0
 
 * 13-Aug-2018
 * First v2 release
-
-
-
-
-

R/script.R

@@ -12,6 +12,11 @@
 #' library(pophelperShiny)
 #' runPophelper()
 #' }
+#' @import ggplot2
+#' @import highcharter
+#' @import magrittr
+#' @import pophelper
+#' @importFrom shiny actionButton br checkboxInput column conditionalPanel div downloadButton downloadHandler eventReactive fileInput fluidRow fluidPage h1 h2 h3 h4 h5 h6 helpText hr HTML htmlOutput imageOutput incProgress inputPanel isolate mainPanel numericInput observe observeEvent Progress reactive reactiveValues renderImage renderPlot renderPrint renderTable renderText renderUI req runApp selectInput selectizeInput setProgress sidebarLayout sidebarPanel sliderInput submitButton tabPanel tabsetPanel tags tagList textInput titlePanel uiOutput updateActionButton updateCheckboxInput updateNumericInput updateSelectInput updateSelectizeInput updateSliderInput updateTextInput validate verbatimTextOutput wellPanel withProgress
 #' @importFrom colourpicker colourInput updateColourInput
 #' @importFrom DT renderDataTable dataTableOutput
 #' @importFrom gridExtra grid.arrange
@@ -34,3 +39,4 @@ runPophelper <- function(display.mode="normal",launch.browser=TRUE,...) {
 
   shiny::runApp(appDir,display.mode=display.mode,launch.browser=launch.browser,...)
 }
+

README.md

@@ -1,15 +1,17 @@
-<img src="man/figures/logo.png" align="right" width="96" height="96">
-
-# pophelperShiny
-
-`pophelperShiny` is an interactive shiny application to use the R package pophelper interactively. This is packaged as an R package to enable easy installation. See the [project website](http://royfrancis.github.io/pophelperShiny) for more details.
-
-### Disclaimer
-
-The `pophelperShiny` R package is offered free and without warranty of any kind, either expressed or implied. I will not be held liable to you for any damage arising out of the use, modification or inability to use this program. `pophelperShiny` R package can be used, redistributed and/or modified freely for non-commercial purposes subject to the original source being properly cited. Licensed under GPL-3. Please make sure you verify all your results.  
-
-### Contact
-
-If you have an comments, suggestions, corrections or ideas on ways to improve or extend this package, feel free to contact me. Submit an issue on the [Github issues page](https://github.com/royfrancis/pophelperShiny/issues).  
-
-2019 | Roy M Francis  
+<img src="man/figures/logo.png" align="right" width="96" height="96">
+
+# pophelperShiny
+
+[![ci_badge](https://github.com/royfrancis/pophelperShiny/workflows/build/badge.svg)](https://github.com/royfrancis/pophelperShiny/actions?workflow=build) [![Docker Image Size (latest by date)](https://img.shields.io/docker/image-size/royfrancis/pophelpershiny?label=dockerhub)](https://hub.docker.com/repository/docker/royfrancis/pophelpershiny)
+
+`pophelperShiny` is an interactive shiny application to use the R package pophelper interactively. This is packaged as an R package to enable easy installation. See the [project website](http://royfrancis.github.io/pophelperShiny) for more details.
+
+### Disclaimer
+
+This R package is offered free and without warranty of any kind, either expressed or implied. I will not be held liable to you for any damage arising out of the use, modification or inability to use this program. This R package can be used, redistributed and/or modified freely for non-commercial purposes subject to the original source being properly cited. Licensed under GPL-3. Please make sure you verify all your results.  
+
+### Contact
+
+If you have an comments, suggestions, corrections or ideas on ways to improve or extend this package, feel free to contact me. Submit an issue on the [Github issues page](https://github.com/royfrancis/pophelperShiny/issues).  
+
+2021 | Roy M Francis  

_pkgdown.yml

@@ -0,0 +1,34 @@
+title: pophelperShiny
+url: https://github.com/royfrancis/pophelperShiny
+template:
+  params:
+    bootswatch: flatly
+
+navbar:
+  structure:
+    left:
+    - home
+    - articles
+    - reference
+    - news
+    right:
+    - github
+  components:
+    home:
+      icon: fa-home fa-lg
+      href: index.html
+    articles:
+      text: "Guide"
+      icon: fa-tools
+      href: articles/index.html
+    reference:
+      text: Reference
+      icon: fa-book
+      href: reference/index.html
+    news:
+      text: Versions
+      icon: fa-history
+      href: news/index.html
+    github:
+      icon: fa-github fa-lg
+      href: https://github.com/royfrancis/pophelperShiny