Improve and extend importers

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: miaDash
-Version: 1.1.1
+Version: 1.1.2
 Authors@R: 
     c(person(given = "Giulio", family = "Benedetti", role = c("aut", "cre"),
            email = "giulio.benedetti@utu.fi",
@@ -25,7 +25,6 @@ Depends:
     shiny
 Imports:
     ape,
-    biomformat,
     htmltools,
     iSEEtree (>= 1.1.4),
     mia,

NAMESPACE

@@ -8,7 +8,6 @@ importFrom(SummarizedExperiment,colData)
 importFrom(TreeSummarizedExperiment,TreeSummarizedExperiment)
 importFrom(TreeSummarizedExperiment,rowTree)
 importFrom(ape,read.tree)
-importFrom(biomformat,read_biom)
 importFrom(htmltools,HTML)
 importFrom(htmltools,br)
 importFrom(htmltools,div)
@@ -28,9 +27,12 @@ importFrom(iSEEtree,RowTreePlot)
 importFrom(iSEEtree,ScreePlot)
 importFrom(mia,addAlpha)
 importFrom(mia,agglomerateByRank)
-importFrom(mia,convertFromBIOM)
 importFrom(mia,getDissimilarity)
+importFrom(mia,importBIOM)
+importFrom(mia,importHUMAnN)
 importFrom(mia,importMetaPhlAn)
+importFrom(mia,importMothur)
+importFrom(mia,importQIIME2)
 importFrom(mia,runNMDS)
 importFrom(mia,runRDA)
 importFrom(mia,subsetByPrevalent)
@@ -51,4 +53,5 @@ importFrom(stats,as.formula)
 importFrom(utils,data)
 importFrom(utils,packageVersion)
 importFrom(utils,read.csv)
+importFrom(utils,read.table)
 importFrom(vegan,vegdist)

NEWS

@@ -1,24 +1,28 @@
-Changes in version 0.1.0
-* Initialised app
-* Added import functionality
+Changes in version 1.1.2
+* Added importers for HUMAnN, QIIME2 and Mothur
+* Improved biom importer
 
-Changes in version 0.2.0
-* Added manipulate functionality
-* Added estimate functionality
-* Added panel layout customisation
-* Added unit testing
+Changes in version 0.99.12
+* Fixed tab title
 
-Changes in version 0.99.2
-* Moved to shinydashboard
+Changes in version 0.99.5
+* Implemented error check system
+* Added mia logo
 
 Changes in version 0.99.3
 * Added tree import option
 * Fixed bugs with RDS and unifrac
 * Added clickable title box
 
-Changes in version 0.99.5
-* Implemented error check system
-* Added mia logo
+Changes in version 0.99.2
+* Moved to shinydashboard
 
-Changes in version 0.99.12
-* Fixed tab title
+Changes in version 0.2.0
+* Added manipulate functionality
+* Added estimate functionality
+* Added panel layout customisation
+* Added unit testing
+
+Changes in version 0.1.0
+* Initialised app
+* Added import functionality

R/landing_page.R

@@ -73,36 +73,54 @@
 
                         tabPanel(title = "Foreign", value = "foreign", br(),
 
-                            radioButtons(inputId = "ftype",
-                                label = "Type:", choices = list("biom", "QZA",
-                                "MetaPhlAn"), inline = TRUE),
+                            radioButtons(inputId = "ftype", label = "Type:",
+                                choices = list("biom", "HUMAnN", "MetaPhlAn",
+                                "Mothur", "QIIME2"), inline = TRUE),
 
                             fileInput(inputId = "main.file",
                                 label = "Main file:", accept = c(".biom",
-                                ".QZA", ".txt"),
-                                placeholder = "biom, QZA or txt"),
+                                ".tsv", ".shared", ".QZA", ".txt"),
+                                placeholder = "biom, tsv, shared, QZA or txt"),
                             div(style = "margin-top: -20px"),
-
+
+                            fileInput(inputId = "col.data", label = "colData:",
+                                accept = c(".tsv", ".design"),
+                                placeholder = "tsv or design"),
+                            div(style = "margin-top: -20px"),
+
                             conditionalPanel(
-                                condition = "input.ftype == 'biom'",
+                                condition = "input.ftype == 'Mothur' | input.ftype == 'QIIME2'",
 
+                                fileInput(inputId = "f.rowdata",
+                                    label = "rowData:", accept = c(".taxonomy",
+                                    ".qza"), placeholder = "taxonomy or qza"),
+                                div(style = "margin-top: -20px")),
+
+                            conditionalPanel(
+                                condition = "input.ftype == 'biom' | input.ftype == 'MetaPhlAn'",
+
+                                fileInput(inputId = "tree.file",
+                                    label = "rowTree:", placeholder = "tree.tree",
+                                    accept = c(".tree", ".tre", ".qza")),
+                                div(style = "margin-top: -20px")),
+
+                            conditionalPanel(
+                                condition = "input.ftype == 'biom' | input.ftype == 'HUMAnN'",
+
                                 checkboxInput(inputId = "rm.tax.pref",
-                                    label = "Remove taxa prefixes"),
-
+                                    label = "Remove taxa prefixes")),
+
+                            conditionalPanel(
+                                condition = "input.ftype == 'biom'",
+
                                 checkboxInput(inputId = "rank.from.pref",
                                     label = "Derive taxa from prefixes")),
-                             
+
                             conditionalPanel(
-                                condition = "input.ftype == 'MetaPhlAn'",
-
-                                fileInput(inputId = "col.data",
-                                    label = "colData:", accept = ".tsv",
-                                    placeholder = "coldata.tsv"),
-                                div(style = "margin-top: -20px"),
-
-                                fileInput(inputId = "tree.file",
-                                    label = "Tree:", placeholder = "tree.tree",
-                                    accept = c(".tree", ".tre"))))),
+                                condition = "input.ftype == 'HUMAnN'",
+
+                                checkboxInput(inputId = "rm.hum.suf",
+                                    label = "Remove sample suffix")))),
 
                     actionButton("import", "Upload", class = "btn-primary")),
 

R/observers.R

@@ -17,11 +17,11 @@
 #' @importFrom utils read.csv
 #' @importFrom ape read.tree
 #' @importFrom S4Vectors DataFrame
-#' @importFrom biomformat read_biom
-#' @importFrom mia convertFromBIOM importMetaPhlAn
+#' @importFrom mia importHUMAnN importMetaPhlAn importQIIME2 importMothur
+#'   addAlpha
 #' @importFrom TreeSummarizedExperiment TreeSummarizedExperiment
 .create_import_observers <- function(input, rObjects) {
-  
+
     # nocov start
     observeEvent(input$import, {
 
@@ -72,33 +72,58 @@
 
             isolate({
                 req(input$main.file)
-
+
+                coldata <- .set_optarg(input$col.data$datapath,
+                    alternative = input$col.data$datapath)
+
+                treefile <- .set_optarg(input$tree.file$datapath,
+                    alternative = input$tree.file$datapath)
+
                 if( input$ftype == "biom" ){
 
-                    biom_object <- read_biom(input$main.file$datapath)
-
-                    fun_args <- list(x = biom_object,
+                    fun_args <- list(file = input$main.file$datapath,
+                        col.data = coldata, tree.file = treefile,
                         removeTaxaPrefixes = input$rm.tax.pref,
                         rankFromPrefix = input$rank.from.pref)
-
+                    
                     rObjects$tse <- .update_tse(
-                        rObjects$tse, convertFromBIOM, fun_args
+                        rObjects$tse, .importBIOM, fun_args
                     )
 
-                } else if( input$ftype == "MetaPhlAn" ){
-
-                    coldata <- .set_optarg(input$col.data$datapath,
-                        alternative = input$col.data$datapath)
+                }else if( input$ftype == "HUMAnN" ){
+
+                    fun_args <- list(file = input$main.file$datapath,
+                        col.data = coldata,
+                        prefix.rm = input$rm.tax.pref,
+                        remove.suffix = input$rm.hum.suf)
 
-                    treefile <- .set_optarg(input$tree.file$datapath)
-
+                    rObjects$tse <- .update_tse(
+                        rObjects$tse, importHUMAnN, fun_args
+                    )
+
+                }else if( input$ftype == "MetaPhlAn" ){
+
                     fun_args <- list(file = input$main.file$datapath,
                         col.data = coldata, tree.file = treefile)
 
                     rObjects$tse <- .update_tse(
-                         rObjects$tse, importMetaPhlAn, fun_args
-                    ) 
-
+                        rObjects$tse, importMetaPhlAn, fun_args
+                    )
+
+                }else if( input$ftype %in% c("Mothur", "QIIME2") ){
+
+                    imp_fun <- eval(parse(text = paste0("import", input$ftype)))
+
+                    rowdata <- .set_optarg(input$f.rowdata$datapath,
+                        alternative = input$f.rowdata$datapath)
+
+                    fun_args <- list(assay.file = input$main.file$datapath,
+                        row.file = input, col.file = rowdata)
+
+                    rObjects$tse <- .update_tse(
+                        rObjects$tse, imp_fun, fun_args
+                    )
+
                 }
 
             })

R/utils.R

@@ -116,4 +116,25 @@ NULL
 
     cond <- all(vars %in% names(colData(tse)))
     return(cond)
+}
+
+#' @importFrom mia importBIOM
+#' @importFrom S4Vectors DataFrame
+#' @importFrom ape read.tree
+#' @importFrom utils read.table
+.importBIOM <- function(file, col.data = NULL, tree.file = NULL, ...){
+
+    tse <- importBIOM(file, ...)
+
+    if( !is.null(col.data) ){
+        coldata <- read.table(file = col.data, header = TRUE, sep = "\t")
+        rownames(coldata) <- colnames(tse)
+        colData(tse) <- DataFrame(coldata)
+    }
+
+    if( !is.null(tree.file) ){
+        rowTree(tse) <- read.tree(tree.file)
+    }
+
+    return(tse)
 }