Added tree import and fixed unifrac and RDS bugs

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: miaDash
-Version: 0.99.2
+Version: 0.99.3
 Authors@R: 
     c(person(given = "Giulio", family = "Benedetti", role = c("aut", "cre"),
            email = "[email protected]",
@@ -23,6 +23,7 @@ Depends:
     R (>= 4.4.0),
     iSEE
 Imports:
+    ape,
     biomformat,
     htmltools,
     iSEEtree,

NAMESPACE

@@ -12,9 +12,11 @@ importFrom(TreeSummarizedExperiment,TreeSummarizedExperiment)
 importFrom(TreeSummarizedExperiment,colLinks)
 importFrom(TreeSummarizedExperiment,rowLinks)
 importFrom(TreeSummarizedExperiment,rowTree)
+importFrom(ape,read.tree)
 importFrom(biomformat,read_biom)
 importFrom(htmltools,HTML)
 importFrom(htmltools,br)
+importFrom(htmltools,div)
 importFrom(htmltools,tags)
 importFrom(iSEE,ColumnDataTable)
 importFrom(iSEE,ComplexHeatmapPlot)

NEWS

@@ -7,3 +7,10 @@ Changes in version 0.2.0
 * Added estimate functionality
 * Added panel layout customisation
 * Added unit testing
+
+Changes in version 0.99.2
+* Moved to shinydashboard
+
+Changes in version 0.99.3
+* Added tree import option
+* Fixed bugs with RDS and unifrac

R/landing_page.R

@@ -16,7 +16,7 @@
 #'   conditionalPanel
 #' @importFrom shinydashboard dashboardPage dashboardHeader dashboardSidebar
 #'   dashboardBody box
-#' @importFrom htmltools HTML br tags
+#' @importFrom htmltools HTML br tags div
 #' @importFrom shinyjs disable
 #' @importFrom utils data
 .landing_page <- function(FUN, input, output, session) {
@@ -54,22 +54,36 @@
 
                             fileInput(inputId = "assay", label = "Assays:",
                                 accept = ".csv", multiple = TRUE),
+                            div(style = "margin-top: -25px"),
 
                             fileInput(inputId = "coldata", label = "colData:",
                                 accept = ".csv"),
-
+                            div(style = "margin-top: -25px"),
+
                             fileInput(inputId = "rowdata", label = "rowData:",
-                                accept = ".csv")),
+                                accept = ".csv"),
+                            div(style = "margin-top: -25px"),
+
+                            fileInput(inputId = "row.tree",
+                                  label = "rowTree:",
+                                  accept = c(".tree", ".tre")),
+                            div(style = "margin-top: -25px"),
+
+                            fileInput(inputId = "col.tree",
+                                  label = "colTree:",
+                                  accept = c(".tree", ".tre")),
+                            div(style = "margin-top: -25px")),
 
                         tabPanel(title = "Foreign", value = "foreign", br(),
 
                             radioButtons(inputId = "ftype",
                                 label = "Type:", choices = list("biom", "QZA",
-                                "MetaPhlAn")),
+                                "MetaPhlAn"), inline = TRUE),
 
                             fileInput(inputId = "main.file",
                                 label = "Main file:", accept = c(".biom",
                                 ".QZA", ".txt")),
+                            div(style = "margin-top: -25px"),
 
                             conditionalPanel(
                                 condition = "input.ftype == 'biom'",
@@ -85,9 +99,11 @@
 
                                 fileInput(inputId = "col.data",
                                     label = "colData:", accept = ".tsv"),
+                                div(style = "margin-top: -25px"),
 
                                 fileInput(inputId = "tree.file",
-                                    label = "Tree:", accept = ".tree")))),
+                                    label = "Tree:",
+                                    accept = c(".tree", ".tre"))))),
 
                     actionButton("import", "Upload", class = "btn-primary")),
 

R/observers.R

@@ -15,6 +15,7 @@
 
 #' @rdname create_observers
 #' @importFrom utils read.csv
+#' @importFrom ape read.tree
 #' @importFrom S4Vectors DataFrame
 #' @importFrom shiny isolate observeEvent req
 #' @importFrom biomformat read_biom
@@ -33,8 +34,7 @@
 
             isolate({
                 req(input$file)
-                load(file = input$file$datapath)
-                rObjects$tse <- readRDS(gsub(".rds", "", input$file$name))
+                rObjects$tse <- readRDS(input$file$datapath)
             })
 
         }else if( input$format == "raw" ){
@@ -45,23 +45,20 @@
                 assay_list <- lapply(input$assay$datapath,
                     function(x) as.matrix(read.csv(x, row.names = 1)))
 
-                if( !is.null(input$coldata) ){
-                    coldata <- read.csv(input$coldata$datapath, row.names = 1)
-                } else {
-                    coldata <- DataFrame(row.names = colnames(assay_list[[1]]))
-                }
-
-
-                if( !is.null(input$rowdata) ){
-                    rowdata <- read.csv(input$rowdata$datapath, row.names = 1)
-                } else {
-                    rowdata <- NULL
-                }
-
                 names(assay_list) <- gsub(".csv", "", input$assay$name)
 
+                coldata <- .set_optarg(input$coldata$datapath, read.csv,
+                    alternative = DataFrame(row.names = colnames(assay_list[[1]])),
+                    row.names = 1)
+
+                rowdata <- .set_optarg(input$rowdata$datapath, read.csv,
+                    row.names = 1)
+
+                row.tree <- .set_optarg(input$row.tree$datapath, read.tree)
+                col.tree <- .set_optarg(input$col.tree$datapath, read.tree)
+
                 fun_args <- list(assays = assay_list, colData = coldata,
-                    rowData = rowdata)
+                    rowData = rowdata, rowTree = row.tree, colTree = col.tree)
 
                 rObjects$tse <- .update_tse(TreeSummarizedExperiment, fun_args)
             })
@@ -250,9 +247,14 @@
 
                 if( input$beta.index == "unifrac" ){
 
+                    if( is.null(rowTree(rObjects$tse)) ){
+                        .print_message("Unifrac cannot be computed without a rowTree.")
+                        return()
+                    }
+
                     beta_args <- c(beta_args, FUN = getDissimilarity,
-                        tree = rowTree(rObjects$tse), ntop = nrow(rObjects$tse),
-                        method = input$beta.index)
+                        tree = list(rowTree(rObjects$tse)),
+                        ntop = nrow(rObjects$tse), method = input$beta.index)
 
                 } else if( input$bmethod %in% c("MDS", "NMDS") ){
 
@@ -276,8 +278,9 @@
                         formula = as.formula(input$rda.formula))
 
                 }
-
+                print(beta_args)
                 beta_fun <- eval(parse(text = paste0("run", input$bmethod)))
+                print(beta_fun)
                 rObjects$tse <- .update_tse(beta_fun, beta_args)
 
             })

R/utils.R

@@ -51,6 +51,18 @@
     # nocov end
 }
 
+#' @rdname utils
+.set_optarg <- function(item, loader, alternative = NULL, ...){
+
+    if( !is.null(item) ){
+        out <- loader(item, ...)
+    } else {
+        out <- alternative
+    }
+
+    return(out)
+}
+
 #' @rdname utils
 #' @importFrom SummarizedExperiment colData
 .check_formula <- function(form, se){