Merge pull request #35 from Breeding-Insight/development

Bug fixes

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: BIGapp
 Title: Breeding Insight Genomics Shiny Application
-Version: 0.5.0
+Version: 0.5.1
 Authors@R: 
     c(
               person(c("Alexander", "M."), "Sandercock",
@@ -52,7 +52,6 @@ Imports:
     AGHmatrix,
     factoextra,
     future,
-    methods,
     shinycssloaders,
     RColorBrewer,
     tibble,

NAMESPACE

@@ -69,7 +69,6 @@ importFrom(graphics,strwidth)
 importFrom(graphics,text)
 importFrom(graphics,title)
 importFrom(matrixcalc,is.positive.definite)
-importFrom(methods,new)
 importFrom(plotly,add_markers)
 importFrom(plotly,layout)
 importFrom(plotly,plot_ly)

R/app_ui.R

@@ -74,7 +74,7 @@ app_ui <- function(request) {
         ),
         left = div(
           style = "display: flex; align-items: center; height: 100%;",  # Center the version text vertically
-          "v0.5.0")
+          "v0.5.1")
       ),
       dashboardBody(
         disconnectMessage(), #Adds generic error message for any error if not already accounted for

R/mod_GSAcc.R

@@ -791,6 +791,7 @@ mod_GSAcc_server <- function(id){
       validate(
         need(!is.null(pred_outputs$avg_GEBVs), "Upload the input files, set the parameters and click 'run analysis' to access results in this session.")
       )
+      pred_outputs$avg_GEBVs
     })
 
     output$pred_gebvs_table <- renderDT({avg_GEBVs()}, options = list(scrollX = TRUE,autoWidth = FALSE, pageLength = 5))

R/mod_dapc.R

@@ -103,11 +103,9 @@ mod_dapc_ui <- function(id){
 
 #' dapc Server Functions
 #' @import grDevices
-#' @importFrom methods new
 #' @importFrom graphics axis
 #' @importClassesFrom adegenet genlight
 #' @importFrom adegenet find.clusters dapc optim.a.score pop<- nInd scatter.dapc
-#' @importFrom methods new
 #' @importFrom vcfR read.vcfR extract.gt
 #' @importFrom stats BIC as.formula lm logLik median model.matrix na.omit prcomp qbeta quantile runif sd setNames
 #' @noRd
@@ -129,7 +127,7 @@ mod_dapc_server <- function(id){
     observeEvent(input$K_start, {
 
       toggleClass(id = "dapc_ploidy", class = "borderred", condition = (is.na(input$dapc_ploidy) | is.null(input$dapc_ploidy)))
-      if (is.null(input$dosage_file1$datapath)) {
+      if (is.null(input$dosage_file$datapath)) {
         shinyalert(
           title = "Missing input!",
           text = "Upload VCF File",
@@ -145,11 +143,11 @@ mod_dapc_server <- function(id){
           animation = TRUE
         )
       }
-      req(input$dosage_file1$datapath, input$dapc_ploidy)
+      req(input$dosage_file$datapath, input$dapc_ploidy)
 
       ploidy <- as.numeric(input$dapc_ploidy)
       maxK <- as.numeric(input$dapc_kmax)
-      geno <- input$dosage_file1$datapath
+      geno <- input$dosage_file$datapath
 
       ##Add in VCF with the vcfR package (input VCF, then convert to genlight using vcf2genlight function)
 
@@ -185,11 +183,10 @@ mod_dapc_server <- function(id){
 
     observeEvent(input$dapc_start, {
 
-      if(is.null(input$dosage_file2)) dosage_file2 <- input$dosage_file1$datapath
       toggleClass(id = "dapc_ploidy", class = "borderred", condition = (is.na(input$dapc_ploidy) | is.null(input$dapc_ploidy)))
       toggleClass(id = "dapc_k", class = "borderred", condition = (is.na(input$dapc_k) | is.null(input$dapc_k)))
 
-      if (is.null(dosage_file2)) {
+      if (is.null(input$dosage_file$datapath)) {
         shinyalert(
           title = "Missing input!",
           text = "Upload VCF File",
@@ -205,9 +202,9 @@ mod_dapc_server <- function(id){
           animation = TRUE
         )
       }
-      req(dosage_file2, input$dapc_ploidy, input$dapc_k)
+      req(input$dosage_file$datapath, input$dapc_ploidy, input$dapc_k)
 
-      geno <- dosage_file2
+      geno <- input$dosage_file$datapath
       ploidy <- as.numeric(input$dapc_ploidy)
       selected_K <- as.numeric(input$dapc_k)
 
@@ -312,6 +309,7 @@ mod_dapc_server <- function(id){
       validate(
         need(!is.null(dapc_items$assignments), "Input VCF, define parameters and click `run analysis` in Step 2:(DAPC) to access results in this session.")
       )
+      dapc_items$assignments
     })
 
     output$DAPC_table <- renderDT({

README.md

@@ -1,8 +1,14 @@
-# (B)reeding (I)nsight (G)enomics app
+<!-- badges: start -->
+[![R-CMD-check](https://github.com/Breeding-Insight/BIGapp/workflows/R-CMD-check/badge.svg)](https://github.com/Breeding-Insight/BIGapp/actions)
+[![Development](https://img.shields.io/badge/development-active-blue.svg)](https://img.shields.io/badge/development-active-blue.svg)
+  <!-- badges: end -->
+
+# (B)reeding (I)nsight (G)enomics app <img src="https://github.com/user-attachments/assets/60955106-fa99-4495-9c8a-c6a7d0b5ed48" align="right" width="250"/>
 
 Currently, Breeding Insight provides bioinformatic processing support for our external collaborators. This R shiny app will provide a web-based user friendly way for our internal and external collaborators to analyze genomic data without needing to use command-line tools.
 
 ### Supported Analyses
+
 Initial supported analyses will include the mature genomics/bioinformatics pipelines developed within Breeding Insight, with additional analyses continuing to be added.
 
 Supported:
@@ -27,6 +33,9 @@ Supported:
 Tutorial available: 
 https://scribehow.com/page/BIGapp_Tutorials__FdLsY9ZxQsi6kgT9p-U2Zg
 
+Online preview:
+https://big-demo.shinyapps.io/bigapp/
+
 **Local computer**
 1. Install R
 2. Open Terminal (on mac)
@@ -41,25 +50,23 @@ BIGapp::run_app()
 
 **Online (in progress)**
 
-## References
+## Third-party software
+
 The BIG app relies on both custom scripts and previously developed R packages cited below:
 
-R: version 4.2.2
+* [R](): version 4.2.2
+
+#### R packages
+
+* Shiny tools: [shiny](https://cran.r-project.org/web/packages/shiny/index.html), [shinyWidgets](https://cran.r-project.org/web/packages/shinyWidgets/index.html), [shinyalert](https://cran.r-project.org/web/packages/shinyalert/index.html), [shinyjs](https://cran.r-project.org/web/packages/shinyjs/index.html), [shinydisconnect](https://cran.r-project.org/web/packages/shinydisconnect/index.html), [shinycssloaders](https://cran.r-project.org/web/packages/shinycssloaders/index.html), [bs4Dash](https://cran.r-project.org/web/packages/bs4Dash/index.html),  [DT](https://cran.r-project.org/web/packages/DT/index.html), [config](https://cran.r-project.org/web/packages/config/index.html)
 
-required_cran_packages <- c("updog", "ggplot2","devtools","GWASpoly","SNPRelate",
-                       "adegenet", "future", "scales", "AGHmatrix", "stats", 
-                       "factoextra", "readxl", "ggrepel", "dplyr", "shiny",
-                       "shinydashboard","randomcoloR","plotly", "DT","RColorBrewer",
-                       "dichromat", "bs4Dash", "shinyWidgets","data.table",
-                       "matrixcalc","Matrix", "shinyalert","rrBLUP", "tidyverse",
-                       "foreach", "doParallel","VariantAnnotation", "vcfR")
+* Genetic analysis: [updog](https://cran.r-project.org/web/packages/updog/index.html), [GWASpoly](https://github.com/jendelman/GWASpoly), [AGHmatrix](https://cran.r-project.org/web/packages/AGHmatrix/index.html), [rrBLUP](https://cran.r-project.org/web/packages/rrBLUP/index.html), [BIGr](https://github.com/Breeding-Insight/BIGr), [adegenet](https://cran.r-project.org/web/packages/adegenet/index.html), [vcfR](https://cran.r-project.org/web/packages/vcfR/index.html)
 
-required_bio_packages <- c("SNPRelate","VariantAnnotation")
+* Data manipulation optimization: [dplyr](https://cran.r-project.org/web/packages/dplyr/index.html), [tidyr](https://cran.r-project.org/web/packages/tidyr/index.html), [purrr](https://cran.r-project.org/web/packages/purrr/index.html), [stringr](https://cran.r-project.org/web/packages/stringr/index.html), [future](https://cran.r-project.org/web/packages/future/index.html), [tibble](https://cran.r-project.org/web/packages/tibble/vignettes/tibble.html)
 
-Dev_tools_packages <- c("GWASpoly")
+* Statistical analysis: [factoextra](https://cran.r-project.org/web/packages/factoextra/index.html), [MASS](https://cran.r-project.org/web/packages/MASS/index.html), [Matrix](https://cran.r-project.org/web/packages/Matrix/index.html), [matrixcalc](https://cran.r-project.org/web/packages/matrixcalc/index.html)
 
-if (!require("BiocManager", quietly = TRUE))
-    install.packages("BiocManager")
+* Generate pretty graphics: [ggplot2](https://cran.r-project.org/web/packages/ggplot2/index.html), [scales](https://cran.r-project.org/web/packages/scales/index.html), [RColorBrewer](https://cran.r-project.org/web/packages/RColorBrewer/index.html), [plotly](https://cran.r-project.org/web/packages/plotly/index.html)
 
 
 ## Funding Sources