Merge pull request #14 from microbiome/bioc_review

Use bibtex citations in vignettes and add shiny to Depends

Author: RiboRings

Diff for: DESCRIPTION

@@ -1,5 +1,5 @@
 Package: miaDash
-Version: 0.99.5
+Version: 0.99.6
 Authors@R: 
     c(person(given = "Giulio", family = "Benedetti", role = c("aut", "cre"),
            email = "[email protected]",
@@ -21,7 +21,8 @@ License: Artistic-2.0
 Encoding: UTF-8
 Depends:
     R (>= 4.4.0),
-    iSEE
+    iSEE,
+    shiny
 Imports:
     ape,
     biomformat,
@@ -31,7 +32,6 @@ Imports:
     mia,
     rintrojs,
     scater,
-    shiny,
     shinydashboard,
     shinyjs,
     S4Vectors,

Diff for: NAMESPACE

@@ -45,35 +45,6 @@ importFrom(mia,transformAssay)
 importFrom(rintrojs,introjs)
 importFrom(scater,runMDS)
 importFrom(scater,runPCA)
-importFrom(shiny,actionButton)
-importFrom(shiny,addResourcePath)
-importFrom(shiny,checkboxInput)
-importFrom(shiny,conditionalPanel)
-importFrom(shiny,downloadButton)
-importFrom(shiny,downloadHandler)
-importFrom(shiny,fileInput)
-importFrom(shiny,fluidRow)
-importFrom(shiny,isolate)
-importFrom(shiny,modalDialog)
-importFrom(shiny,numericInput)
-importFrom(shiny,observe)
-importFrom(shiny,observeEvent)
-importFrom(shiny,radioButtons)
-importFrom(shiny,reactiveValues)
-importFrom(shiny,renderPrint)
-importFrom(shiny,renderUI)
-importFrom(shiny,req)
-importFrom(shiny,selectInput)
-importFrom(shiny,showModal)
-importFrom(shiny,showNotification)
-importFrom(shiny,sliderInput)
-importFrom(shiny,tabPanel)
-importFrom(shiny,tabsetPanel)
-importFrom(shiny,textInput)
-importFrom(shiny,updateNumericInput)
-importFrom(shiny,updateSelectInput)
-importFrom(shiny,verbatimTextOutput)
-importFrom(shiny,wellPanel)
 importFrom(shinydashboard,box)
 importFrom(shinydashboard,dashboardBody)
 importFrom(shinydashboard,dashboardHeader)

Diff for: R/landing_page.R

@@ -10,10 +10,6 @@
 #' @keywords internal
 
 #' @rdname landing_page
-#' @importFrom shiny actionButton fluidRow tabPanel tabsetPanel renderUI
-#'   selectInput sliderInput textInput wellPanel reactiveValues radioButtons
-#'   numericInput fileInput checkboxInput verbatimTextOutput downloadButton
-#'   conditionalPanel
 #' @importFrom shinydashboard dashboardPage dashboardHeader dashboardSidebar
 #'   dashboardBody box
 #' @importFrom htmltools HTML br tags div tagList
@@ -48,29 +44,30 @@
                         tabPanel(title = "R Object", value = "rds", br(),
 
                             fileInput(inputId = "file", label = "RDS:",
-                                accept = ".rds")),
+                                accept = ".rds", placeholder = "object.rds")),
 
                         tabPanel(title = "Raw Data", value = "raw", br(),
 
                             fileInput(inputId = "assay", label = "Assays:",
-                                accept = ".csv", multiple = TRUE),
+                                accept = ".csv", multiple = TRUE,
+                                placeholder = "assay.csv"),
                             div(style = "margin-top: -20px"),
 
                             fileInput(inputId = "coldata", label = "colData:",
-                                accept = ".csv"),
+                                accept = ".csv", placeholder = "coldata.csv"),
                             div(style = "margin-top: -20px"),
 
                             fileInput(inputId = "rowdata", label = "rowData:",
-                                accept = ".csv"),
+                                accept = ".csv", placeholder = "rowdata.csv"),
                             div(style = "margin-top: -20px"),
 
                             fileInput(inputId = "row.tree",
-                                  label = "rowTree:",
+                                  label = "rowTree:", placeholder = "row.tree",
                                   accept = c(".tree", ".tre")),
                             div(style = "margin-top: -20px"),
 
                             fileInput(inputId = "col.tree",
-                                  label = "colTree:",
+                                  label = "colTree:", placeholder = "col.tree",
                                   accept = c(".tree", ".tre")),
                             div(style = "margin-top: -20px")),
 
@@ -82,7 +79,8 @@
 
                             fileInput(inputId = "main.file",
                                 label = "Main file:", accept = c(".biom",
-                                ".QZA", ".txt")),
+                                ".QZA", ".txt"),
+                                placeholder = "biom, QZA or txt"),
                             div(style = "margin-top: -20px"),
 
                             conditionalPanel(
@@ -98,11 +96,12 @@
                                 condition = "input.ftype == 'MetaPhlAn'",
 
                                 fileInput(inputId = "col.data",
-                                    label = "colData:", accept = ".tsv"),
+                                    label = "colData:", accept = ".tsv",
+                                    placeholder = "coldata.tsv"),
                                 div(style = "margin-top: -20px"),
 
                                 fileInput(inputId = "tree.file",
-                                    label = "Tree:",
+                                    label = "Tree:", placeholder = "tree.tree",
                                     accept = c(".tree", ".tre"))))),
 
                     actionButton("import", "Upload", class = "btn-primary")),

Diff for: R/miaDash.R

@@ -22,7 +22,6 @@
 #' @export
 #' @rdname miaDash
 #' @importFrom iSEE iSEE
-#' @importFrom shiny addResourcePath
 #' @importFrom utils packageVersion
 #' @importFrom htmltools tags
 miaDash <- function() {

Diff for: R/observers.R

@@ -17,7 +17,6 @@
 #' @importFrom utils read.csv
 #' @importFrom ape read.tree
 #' @importFrom S4Vectors DataFrame
-#' @importFrom shiny isolate observeEvent req
 #' @importFrom biomformat read_biom
 #' @importFrom mia convertFromBIOM importMetaPhlAn
 #' @importFrom TreeSummarizedExperiment TreeSummarizedExperiment
@@ -113,7 +112,6 @@
 }
 
 #' @rdname create_observers
-#' @importFrom shiny isolate observeEvent req
 #' @importFrom SummarizedExperiment assay
 #' @importFrom mia subsetByPrevalent subsetByRare agglomerateByRank
 #'   transformAssay
@@ -195,7 +193,6 @@
 
 #' @rdname create_observers
 #' @importFrom stats as.formula
-#' @importFrom shiny isolate observeEvent req
 #' @importFrom mia addAlpha runNMDS runRDA getDissimilarity
 #' @importFrom TreeSummarizedExperiment rowTree
 #' @importFrom scater runMDS runPCA
@@ -300,7 +297,6 @@
 }
 
 #' @rdname create_observers
-#' @importFrom shiny updateSelectInput updateNumericInput observe
 #' @importFrom SummarizedExperiment assayNames
 #' @importFrom mia taxonomyRanks
 #' @importFrom rintrojs introjs
@@ -344,7 +340,6 @@
 }
 
 #' @rdname create_observers
-#' @importFrom shiny observeEvent
 .create_launch_observers <- function(FUN, input, session, rObjects) {
 
     # nocov start

Diff for: R/outputs.R

@@ -13,7 +13,6 @@
 #' @keywords internal
 
 #' @rdname render_output
-#' @importFrom shiny renderPrint
 .render_overview <- function(output, rObjects) {
 
     # nocov start
@@ -26,7 +25,6 @@
 }
 
 #' @rdname render_output
-#' @importFrom shiny downloadHandler
 .render_download <- function(output, rObjects) {
 
     # nocov start

Diff for: R/utils.R

@@ -16,7 +16,6 @@
 }
 
 #' @rdname utils
-#' @importFrom shiny showNotification
 .update_tse <- function(tse, fun, fun_args) {
 
     tse <- tryCatch({withCallingHandlers({
@@ -41,7 +40,6 @@
 }
 
 #' @rdname utils
-#' @importFrom shiny showModal modalDialog
 .print_message <- function(..., title = "Invalid input:") {
 
     # nocov start

Diff for: inst/REFERENCES.bib

@@ -0,0 +1,55 @@
+@Manual{core2024r,
+  title = {R: A Language and Environment for Statistical Computing},
+  author = {{R Core Team}},
+  organization = {R Foundation for Statistical Computing},
+  address = {Vienna, Austria},
+  year = {2024},
+  url = {https://www.R-project.org/},
+  }
+
+@misc{benedetti2024iseetree,
+  title={iSEEtree: interactive explorer for hierarchical data}, 
+  author={Giulio Benedetti and Ely Seraidarian and Theotime Pralas and Akewak Jeba and Tuomas Borman and Leo Lahti},
+  year={2024},
+  eprint={2412.02882},
+  archivePrefix={arXiv},
+  primaryClass={cs.MS},
+  url={https://arxiv.org/abs/2412.02882}
+}
+
+@article{rue2018isee,
+  title={iSEE: interactive summarizedexperiment explorer},
+  author={Rue-Albrecht, Kevin and Marini, Federico and Soneson, Charlotte and Lun, Aaron TL},
+  journal={F1000Research},
+  volume={7},
+  year={2018},
+  publisher={Faculty of 1000 Ltd},
+  doi={10.12688/f1000research.14966.1}
+}
+
+@Manual{chang2024shiny,
+    title = {shiny: Web Application Framework for R},
+    author = {Winston Chang and Joe Cheng and JJ Allaire and Carson Sievert and Barret Schloerke and Yihui Xie and Jeff Allen and Jonathan McPherson and Alan Dipert and Barbara Borges},
+    year = {2024},
+    note = {R package version 1.9.1},
+    url = {https://CRAN.R-project.org/package=shiny},
+  }
+
+@Manual{borman2024mia,
+  title = {mia: Microbiome analysis},
+  author = {Tuomas Borman and Felix G.M. Ernst and Sudarshan A. Shetty and Leo Lahti},
+  year = {2024},
+  note = {R package version 1.14.0},
+  url = {https://bioconductor.org/packages/mia},
+  doi = {10.18129/B9.bioc.mia},
+}
+
+@article{huang2020treesummarizedexperiment,
+  title={TreeSummarizedExperiment: a S4 class for data with hierarchical structure},
+  author={Huang, Ruizhu and Soneson, Charlotte and Ernst, Felix GM and Rue-Albrecht, Kevin C and Yu, Guangchuang and Hicks, Stephanie C and Robinson, Mark D},
+  journal={F1000Research},
+  volume={9},
+  year={2020},
+  publisher={Faculty of 1000 Ltd},
+  doi={10.12688/f1000research.26669.2}
+}

Diff for: vignettes/miaDash.Rmd

@@ -14,6 +14,7 @@ output:
         number_sections: true
         self_contained: true
         code_folding: show
+bibliography: ../inst/REFERENCES.bib
 date: "`r doc_date()`"
 package: "`r pkg_ver('miaDash')`"
 vignette: >
@@ -29,21 +30,6 @@ knitr::opts_chunk$set(
 )
 ```
 
-```{r vignetteSetup, echo=FALSE, message=FALSE, warning=FALSE}
-## Bib setup
-library(RefManageR)
-
-## Write bibliography information
-bib <- c(
-    R = citation(),
-    mia = citation("mia")[1],
-    iSEEtree = citation("iSEEtree")[1],
-    iSEE = citation("iSEE")[1],
-    TreeSummarizedExperiment = citation("TreeSummarizedExperiment")[1],
-    shiny = citation("shiny")[1]
-)
-```
-
 # Introduction
 
 This notebook provides a practical introduction to the Microbiome Analysis
@@ -169,12 +155,12 @@ citation("miaDash")
 miaDash originates from the joint effort of the R/Bioconductor community. It is
 mainly based on the following software:
 
-- R `r Citep(bib[["R"]])`, statistical programming language
-- `r Biocpkg("mia")` `r Citep(bib[["mia"]])`, framework for microbiome data analysis
-- `r Biocpkg("iSEEtree")` `r Citep(bib[["iSEEtree"]])`, TreeSummarizedExperiment interactive explorer
-- `r Biocpkg("iSEE")` `r Citep(bib[["iSEE"]])`, SummarizedExperiment interactive explorer
-- `r Biocpkg("TreeSummarizedExperiment")` `r Citep(bib[["TreeSummarizedExperiment"]])`, S4 container for hierarchical data
-- `r CRANpkg("shiny")` `r Citep(bib[["shiny"]])`, web app development in R
+- [R](https://www.r-project.org/), statistical programming language [@core2024r]
+- [mia](https://bioconductor.org/packages/release/bioc/html/mia.html), framework for microbiome data analysis [@borman2024mia]
+- [iSEEtree](https://bioconductor.org/packages/release/bioc/html/iSEEtree.html), TreeSummarizedExperiment interactive explorer [@benedetti2024iseetree]
+- [iSEE](https://bioconductor.org/packages/release/bioc/html/iSEE.html), SummarizedExperiment interactive explorer [@rue2018isee]
+- [TreeSummarizedExperiment](https://bioconductor.org/packages/release/bioc/html/TreeSummarizedExperiment.htmlm), S4 container for hierarchical data [@huang2020treesummarizedexperiment]
+- [shiny](https://cran.r-project.org/web/packages/shiny/index.html), web app development in R [@chang2024shiny]
 
 ## Help
 
@@ -194,9 +180,4 @@ options(width = 120)
 sessionInfo()
 ```
 
-# References
-
-```{r vignetteBiblio, results="asis", echo=FALSE, warning=FALSE, message=FALSE}
-# Print bibliography
-PrintBibliography(bib, .opts = list(hyperlink = "to.doc", style = "html"))
-```
+# References