publishing ok

mmollina · Sep 16, 2022 · e47b6c7 · e47b6c7
1 parent 99257db
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diff --git a/R/functions_upload.R b/R/functions_upload.R
@@ -9,21 +9,60 @@
 #' 
 #' @keywords internal
 prepare_examples <- function(example){
-  viewmap_tetra <- viewqtl_tetra <- NULL
-  if(example == "tetra_map"){
-    load(system.file("ext/viewmap_tetra.rda", package = "viewpoly"))
-    load(system.file("ext/viewqtl_tetra.rda", package = "viewpoly"))
+  if(example != "This will be updated"){
+    files <- list.files(system.file("ext/my_viewpoly_objects/", package = "viewpoly"))
+    ids <- read.csv(system.file("ext/info_data.csv", package = "viewpoly"), header = T)
+    idx <- which(ids$ID == example)
+    obj <- load(system.file(paste0("ext/my_viewpoly_objects/",ids$File[idx]), package = "viewpoly"))
+    obj <- get(obj)
 
-    structure(list(map=viewmap_tetra, 
-                   qtl=viewqtl_tetra,
-                   fasta = "https://gesteira.statgen.ncsu.edu/files/genome-browser/Stuberosum_448_v4.03.fa.gz",
-                   gff3 = "https://gesteira.statgen.ncsu.edu/files/genome-browser/Stuberosum_448_v4.03.gene_exons.gff3.gz",
-                   vcf = NULL,
-                   align = NULL, 
-                   wig = NULL,
-                   version = packageVersion("viewpoly")),
-              class = "viewpoly")
-  }
+    # fasta
+    obj$fasta <- if(ids$fasta[idx] == "NULL") {
+      NULL 
+    }else if(grepl("http", ids$fasta[idx])) {
+      ids$fasta[idx]
+    } else { 
+      system.file(paste0("ext/my_genomes/",ids$fasta[idx]), package = "viewpoly")
+    }
+
+    #gff3
+    obj$gff3 <- if(ids$gff3[idx] == "NULL") {
+      NULL 
+    }else if(grepl("http", ids$gff3[idx])) {
+      ids$gff3[idx]
+    } else { 
+      system.file(paste0("ext/my_genomes/",ids$gff3[idx]), package = "viewpoly")
+    }
+
+    # vcf
+    obj$vcf <- if(ids$vcf[idx] == "NULL") {
+      NULL 
+    }else if(grepl("http", ids$vcf[idx])) {
+      ids$vcf[idx]
+    } else { 
+      system.file(paste0("ext/my_genomes/",ids$vcf[idx]), package = "viewpoly")
+    }
+
+    # align
+    obj$align <- if(ids$align[idx] == "NULL") {
+      NULL 
+    }else if(grepl("http", ids$align[idx])) {
+      ids$align[idx]
+    } else { 
+      system.file(paste0("ext/my_genomes/",ids$align[idx]), package = "viewpoly")
+    }
+
+    # wig
+    obj$wig <- if(ids$wig[idx] == "NULL") {
+      NULL 
+    }else if(grepl("http", ids$wig[idx])) {
+      ids$wig[idx]
+    } else { 
+      system.file(paste0("ext/my_genomes/",ids$wig[idx]), package = "viewpoly")
+    }
+
+    return(obj)
+  } else return(NULL)
 }
 
 #' Converts map information in custom format files to viewmap object
@@ -376,9 +415,9 @@ prepare_diaQTL <- function(scan1_list, scan1_summaries_list, fitQTL_list, BayesC
   idx <- which(sapply(CI, is.null))
   if(length(idx) != 0 | length(BayesCI_list_ord) != dim(qtl_info2)[1]){
     if(length(idx) != 0)
-    CI[[idx]] <- c(NA, NA)
+      CI[[idx]] <- c(NA, NA)
     else  CI[[length(CI) + 1]] <- c(NA, NA)
-
+    
   }
 
   CI <- do.call(rbind, CI)

diff --git a/R/mod_upload.R b/R/mod_upload.R
@@ -24,9 +24,9 @@ mod_upload_ui <- function(id){
       column(width = 12,
              fluidPage(
                box(id= ns("box_example"), width = 12, solidHeader = TRUE, collapsible = TRUE, collapsed = FALSE, status="primary", title = actionLink(inputId = ns("exampleID"), label = tags$b("Available datasets")),
-                   radioButtons(ns("example_map"), label = p("Selected dataset:"), 
-                                choices = c("Potato - Atlantic x B1829-5" = "tetra_map"),
-                                selected = "tetra_map"), br(), br(), hr()
+                   radioButtons(ns("example_map"), label = "Select dataset:", 
+                                choices = "This will be updated",
+                                selected = "This will be updated"), br(), br(), hr()
                )
              )
       )
@@ -59,6 +59,18 @@ mod_upload_server <- function(input, output, session, parent_session){
                       selected = "about")
   })
 
+  # load datas
+  observe({
+    files <- list.files(system.file("ext/my_viewpoly_objects/", package = "viewpoly"))
+    ids <- read.csv(system.file("ext/info_data.csv", package = "viewpoly"), header = T)
+
+    choices <- as.list(ids$ID)
+    names(choices) <- ids$ID
+
+    updateRadioButtons(session, "example_map", label = "Select dataset:", 
+                       choices = choices,
+                       selected = choices[[1]])
+  })
 
   # Wait system for the uploads
   loadExample = reactive({

diff --git a/README.md b/README.md
@@ -75,11 +75,11 @@ It is optional to upload also:
 
 ### Documentation
 
-Access the [tutorial](https://cristianetaniguti.github.io/viewpoly_vignettes/VIEWpoly_tutorial.html). 
+* Access the [tutorial](https://cristianetaniguti.github.io/viewpoly_vignettes/VIEWpoly_tutorial.html). 
 
-We also presented the app main features in [this video](https://www.youtube.com/watch?v=OBt_jebhfeY)
+* We also presented the app main features in [this video](https://www.youtube.com/watch?v=OBt_jebhfeY)
 
-If you would like to contribute to develop `VIEWpoly`, please check our [Contributing Guidelines](https://cristianetaniguti.github.io/viewpoly_vignettes/Contributing_guidelines.html).
+* If you would like to contribute to develop `VIEWpoly`, please check our [Contributing Guidelines](https://cristianetaniguti.github.io/viewpoly_vignettes/Contributing_guidelines.html).
 
 ### References
 

diff --git a/inst/ext/about.Rmd b/inst/ext/about.Rmd
@@ -21,11 +21,13 @@ See more about this population [here](https://www.nature.com/articles/s41437-021
 
 ### Documentation
 
-Access more information about how to make your data sets available through VIEWpoly [here](https://cristianetaniguti.github.io/viewpoly_vignettes/Publish_data_VIEWpoly.html).
+* Access more information about how to make your data sets available through VIEWpoly [here](https://cristianetaniguti.github.io/viewpoly_vignettes/Publish_data_VIEWpoly.html).
 
-Access VIEWpoly tutorial [here](https://cristianetaniguti.github.io/viewpoly_vignettes/VIEWpoly_tutorial.html).
+* Access VIEWpoly tutorial [here](https://cristianetaniguti.github.io/viewpoly_vignettes/VIEWpoly_tutorial.html).
 
-VIEWpoly main features are also presented in this [video](https://www.youtube.com/watch?v=OBt_jebhfeY).
+* VIEWpoly main features are also presented in this [video](https://www.youtube.com/watch?v=OBt_jebhfeY).
+
+* If you would like to contribute to develop `VIEWpoly`, please check our [Contributing Guidelines](https://cristianetaniguti.github.io/viewpoly_vignettes/Contributing_guidelines.html).
 
 ### References
 

diff --git a/inst/ext/beta.hat.tsv.gz b/inst/ext/beta.hat.tsv.gz
diff --git a/inst/ext/blups.tsv.gz b/inst/ext/blups.tsv.gz
diff --git a/inst/ext/dosage.tsv.gz b/inst/ext/dosage.tsv.gz
diff --git a/inst/ext/effects.tsv.gz b/inst/ext/effects.tsv.gz
diff --git a/inst/ext/functions4tests.R b/inst/ext/functions4tests.R
diff --git a/inst/ext/info_data.csv b/inst/ext/info_data.csv
@@ -0,0 +1,4 @@
+File,ID,fasta,gff3,vcf,align,wig
+example_data.RData,Potato - Atlantic x B1829-5 (genome links),https://gesteira.statgen.ncsu.edu/files/genome-browser/Stuberosum_448_v4.03.fa.gz,https://gesteira.statgen.ncsu.edu/files/genome-browser/Stuberosum_448_v4.03.gene_exons.gff3.gz,NULL,NULL,NULL
+example_data.Rdata,Potato - Atlantic x B1829-5 (genome files),Stuberosum_sub.fa.gz,Stuberosum_sub.sorted.gff3.gz,NULL,NULL,NULL
+example_data.RData,Potato - Atlantic x B1829-5 (without genome info),NULL,NULL,NULL,NULL,NULL
diff --git a/inst/ext/map.tsv.gz b/inst/ext/map.tsv.gz
diff --git a/inst/ext/my_genomes/Stuberosum_sub.fa.gz b/inst/ext/my_genomes/Stuberosum_sub.fa.gz
diff --git a/inst/ext/my_genomes/Stuberosum_sub.fa.gz.fai b/inst/ext/my_genomes/Stuberosum_sub.fa.gz.fai
@@ -0,0 +1 @@
+ST4.03ch01	349930	12	70	71
diff --git a/inst/ext/my_genomes/Stuberosum_sub.fa.gz.gzi b/inst/ext/my_genomes/Stuberosum_sub.fa.gz.gzi
diff --git a/inst/ext/my_genomes/Stuberosum_sub.sorted.gff3.gz b/inst/ext/my_genomes/Stuberosum_sub.sorted.gff3.gz
diff --git a/inst/ext/my_genomes/Stuberosum_sub.sorted.gff3.gz.tbi b/inst/ext/my_genomes/Stuberosum_sub.sorted.gff3.gz.tbi
diff --git a/inst/ext/my_viewpoly_objects/example_data.RData b/inst/ext/my_viewpoly_objects/example_data.RData
diff --git a/inst/ext/phases.tsv.gz b/inst/ext/phases.tsv.gz
diff --git a/inst/ext/probs.tsv.gz b/inst/ext/probs.tsv.gz
diff --git a/inst/ext/profile.tsv.gz b/inst/ext/profile.tsv.gz
diff --git a/inst/ext/qtl_info.tsv.gz b/inst/ext/qtl_info.tsv.gz
diff --git a/inst/ext/selected_mks.tsv.gz b/inst/ext/selected_mks.tsv.gz
diff --git a/inst/ext/viewmap_tetra.rda b/inst/ext/viewmap_tetra.rda
diff --git a/inst/ext/viewqtl_tetra.rda b/inst/ext/viewqtl_tetra.rda
diff --git a/inst/tests/shinytest.R b/inst/tests/shinytest.R
diff --git a/inst/tests/shinytest/github_actions_tests.R b/inst/tests/shinytest/github_actions_tests.R