Merge pull request #20 from microbiome/fix

Update iSEEtree compat requirements

Author: RiboRings

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: miaDash
-Version: 0.99.9
+Version: 0.99.11
 Authors@R: 
     c(person(given = "Giulio", family = "Benedetti", role = c("aut", "cre"),
            email = "[email protected]",
@@ -27,7 +27,7 @@ Imports:
     ape,
     biomformat,
     htmltools,
-    iSEEtree,
+    iSEEtree (>= 1.1.4),
     mia,
     rintrojs,
     scater,
@@ -42,6 +42,7 @@ Imports:
 Suggests:
     BiocStyle,
     knitr,
+    philr,
     remotes,
     rmarkdown,
     testthat (>= 3.0.0)

R/constants.R

@@ -1,19 +1,23 @@
 #' Constants
 #'
-#' Constant values used throughout miaDash panels and extensions.
+#' Constant values used throughout the miaDash app.
 #' 
 #' @section Panel layout:
 #' \describe{
 #' \item{\code{.miaDashDefaultPanels}}{List of panel names in the default layout of miaDash.}
 #' \item{\code{.miaDashOtherPanels}}{List of panel names not in the default layout of miaDash.}
+#' \item{\code{.transformMethods}}{List of transformations applicable to assays.}
+#' \item{\code{.alphaMetrics}}{List of alpha diversity metrics.}
+#' \item{\code{.betaMetrics}}{List of beta diversity metrics.}
+#' \item{\code{.betaMethods}}{List of beta diversity methods.}
 #' }
 #'
 #' @author Giulio Benedetti
 #' 
 #' @keywords internal
 #' @name constants
-#' @aliases .miaDashDefaultPanels
-#' .miaDashOtherPanels
+#' @aliases .miaDashDefaultPanels .miaDashOtherPanels .transformMethods
+#' .alphaMetrics .betaMetrics .betaMethods
 NULL
 
 #' @rdname constants
@@ -24,4 +28,26 @@ NULL
 #' @rdname constants
 .miaDashOtherPanels <- c("PrevalencePlot", "RDAPlot", "ScreePlot",
     "LoadingPlot", "ColumnTreePlot", "RowGraphPlot", "ColumnGraphPlot",
-    "RowDataPlot", "ColumnDataPlot")
+    "RowDataPlot", "ColumnDataPlot")
+
+#' @rdname constants
+.transformMethods <- c("alr", "chi.square", "clr", "css", "frequency",
+    "hellinger", "log", "log10", "log2", "max", "normalize", "pa",# "philr",
+    "range", "rank", "rclr", "relabundance", "rrank", "standardize", "total")
+
+#' @rdname constants
+.alphaMetrics <- c("coverage_diversity", "fisher_diversity", "faith_diversity",
+    "gini_simpson_diversity", "inverse_simpson_diversity",
+    "log_modulo_skewness_diversity", "shannon_diversity", "absolute_dominance",
+    "dbp_dominance", "core_abundance_dominance", "gini_dominance",
+    "dmn_dominance", "relative_dominance", "simpson_lambda_dominance",
+    "camargo_evenness", "pielou_evenness", "simpson_evenness", "evar_evenness",
+    "bulla_evenness", "ace_richness", "chao1_richness", "hill_richness",
+    "observed_richness")
+
+#' @rdname constants
+.betaMetrics <- c("euclidean", "bray", "jaccard", "unifrac")
+
+#' @rdname constants
+.betaMethods <- c("MDS", "NMDS", "PCA", "RDA")
+#"TSNE", "UMAP")

R/landing_page.R

@@ -141,8 +141,7 @@
                                 label = "Assay:", choices = NULL),
 
                             selectInput(inputId = "trans.method",
-                                label = "Method:", choices = c("relabundance",
-                                "clr", "standardize")),
+                                label = "Method:", choices = .transformMethods),
 
                             checkboxInput(inputId = "pseudocount",
                                 label = "Pseudocount"),
@@ -168,20 +167,21 @@
 
                             selectInput(inputId = "alpha.index",
                                 label = "Metric:", multiple = TRUE,
-                                choices = c("coverage", "shannon", "faith"))),
+                                choices = .alphaMetrics)),
 
                         tabPanel(title = "Beta", value = "beta",
 
-                            radioButtons(inputId = "bmethod", label = "Method:",
-                                choices = c("MDS", "NMDS", "PCA", "RDA"),
+                            radioButtons(inputId = "bmethod",
+                                label = "Method:", choices = .betaMethods,
                                 inline = TRUE),
 
                             conditionalPanel(
-                                condition = "input.bmethod != 'PCA'",
+                                condition = paste("input.bmethod == 'MDS' || ",
+                                    "input.bmethod == 'NMDS' || ",
+                                    "input.bmethod == 'RDA'"),
 
                                 selectInput(inputId = "beta.index",
-                                    label = "Metric:", choices = c("euclidean",
-                                    "bray", "jaccard", "unifrac"))),
+                                    label = "Metric:", choices = .betaMetrics)),
 
                             conditionalPanel(
                                 condition = "input.bmethod == 'RDA'",

R/miaDash.R

@@ -34,8 +34,7 @@ miaDash <- function() {
             paste0("Microbiome Analysis Dashboard - v", packageVersion("miaDash")),
             tags$img(src = "assets/mia_logo.png", height = "40px", style = "margin-left: 10px"),
             style = "cursor: pointer; font-weight: 500",
-            onclick = "window.location='https://miadash-microbiome.2.rahtiapp.fi/'") 
-            
+            onclick = "window.location='https://miadash-microbiome.2.rahtiapp.fi/'")
     )
 }
 

R/observers.R

@@ -152,17 +152,6 @@
             })
 
         } else if( input$manipulate == "transform" ){
-
-            if( input$trans.method == "clr" && !input$pseudocount &&
-                any(assay(rObjects$tse, input$assay.type) <= 0)){
-              
-                .print_message(
-                    "'clr' cannot be used with non-positive data:",
-                    "please turn on pseudocount."
-                )
-              
-                return()
-            }
 
             isolate({
                 req(input$assay.type)
@@ -177,6 +166,11 @@
                     method = input$trans.method, assay.type = input$assay.type,
                     MARGIN = input$margin, pseudocount = input$pseudocount)
 
+                #if( input$trans.method == "philr" ){
+                #    fun_args <- c(fun_args, tree = list(rowTree(rObjects$tse)),
+                #        node.labels = rowTree(tse)$node.label)
+                #}
+                
                 rObjects$tse <- .update_tse(
                      rObjects$tse, transformAssay, fun_args
                 )

man/constants.Rd

@@ -1,6 +1,10 @@
 destination: docs
 reference:
 - title: App
+- subtitle: Main
 - contents:
   - miaDash
+- subtitle: Other
+- contents:
+  - utils
   - constants