KasperSkytte · September 12, 2023 10:04 · Sep 12, 2023 · Sep 10, 2019
diff --git a/phyloseq_to_ampvis2.R b/phyloseq_to_ampvis2.R
@@ -1,81 +1,3 @@
 phyloseq_to_ampvis2 <- function(physeq) {
-  #check object for class
-  if(!any(class(physeq) %in% "phyloseq"))
-    stop("physeq object must be of class \"phyloseq\"", call. = FALSE)
-
-  #ampvis2 requires taxonomy and abundance table, phyloseq checks for the latter
-  if(is.null(physeq@tax_table))
-    stop("No taxonomy found in the phyloseq object and is required for ampvis2", call. = FALSE)
-
-  #OTUs must be in rows, not columns
-  if(phyloseq::taxa_are_rows(physeq))
-    abund <- as.data.frame(phyloseq::otu_table(physeq)@.Data)
-  else
-    abund <- as.data.frame(t(phyloseq::otu_table(physeq)@.Data))
-
-  #tax_table is assumed to have OTUs in rows too
-  tax <- phyloseq::tax_table(physeq)@.Data
-
-  #merge by rownames (OTUs)
-  otutable <- merge(
-    abund,
-    tax,
-    by = 0,
-    all.x = TRUE,
-    all.y = FALSE,
-    sort = FALSE
-  )
-  colnames(otutable)[1] <- "OTU"
-
-  #extract sample_data (metadata)
-  if(!is.null(physeq@sam_data)) {
-    metadata <- data.frame(
-      phyloseq::sample_data(physeq),
-      row.names = phyloseq::sample_names(physeq), 
-      stringsAsFactors = FALSE, 
-      check.names = FALSE
-    )
-
-    #check if any columns match exactly with rownames
-    #if none matched assume row names are sample identifiers
-    samplesCol <- unlist(lapply(metadata, function(x) {
-      identical(x, rownames(metadata))}))
-
-    if(any(samplesCol)) {
-      #error if a column matched and it's not the first
-      if(!samplesCol[[1]])
-        stop("Sample ID's must be in the first column in the sample metadata, please reorder", call. = FALSE)
-    } else {
-      #assume rownames are sample identifiers, merge at the end with name "SampleID"
-      if(any(colnames(metadata) %in% "SampleID"))
-        stop("A column in the sample metadata is already named \"SampleID\" but does not seem to contain sample ID's", call. = FALSE)
-      metadata$SampleID <- rownames(metadata)
-
-      #reorder columns so SampleID is the first
-      metadata <- metadata[, c(which(colnames(metadata) %in% "SampleID"), 1:(ncol(metadata)-1L)), drop = FALSE]
-    }
-  } else
-    metadata <- NULL
-
-  #extract phylogenetic tree, assumed to be of class "phylo"
-  if(!is.null(physeq@phy_tree)) {
-    tree <- phyloseq::phy_tree(physeq)
-  } else
-    tree <- NULL
-
-  #extract OTU DNA sequences, assumed to be of class "XStringSet"
-  if(!is.null(physeq@refseq)) {
-    #convert XStringSet to DNAbin using a temporary file (easiest)
-    fastaTempFile <- tempfile(pattern = "ampvis2_", fileext = ".fa")
-    Biostrings::writeXStringSet(physeq@refseq, filepath = fastaTempFile)
-  } else
-    fastaTempFile <- NULL
-
-  #load as normally with amp_load
-  ampvis2::amp_load(
-    otutable = otutable,
-    metadata = metadata,
-    tree = tree,
-    fasta = fastaTempFile
-  )
+  stop("The phyloseq_to_ampvis2 function is deprecated. amp_load() now supports loading a phyloseq object directly.", call. = FALSE)
 }
diff --git a/phyloseq_to_ampvis2.R b/phyloseq_to_ampvis2.R
@@ -0,0 +1,81 @@
+phyloseq_to_ampvis2 <- function(physeq) {
+  #check object for class
+  if(!any(class(physeq) %in% "phyloseq"))
+    stop("physeq object must be of class \"phyloseq\"", call. = FALSE)
+
+  #ampvis2 requires taxonomy and abundance table, phyloseq checks for the latter
+  if(is.null(physeq@tax_table))
+    stop("No taxonomy found in the phyloseq object and is required for ampvis2", call. = FALSE)
+
+  #OTUs must be in rows, not columns
+  if(phyloseq::taxa_are_rows(physeq))
+    abund <- as.data.frame(phyloseq::otu_table(physeq)@.Data)
+  else
+    abund <- as.data.frame(t(phyloseq::otu_table(physeq)@.Data))
+
+  #tax_table is assumed to have OTUs in rows too
+  tax <- phyloseq::tax_table(physeq)@.Data
+
+  #merge by rownames (OTUs)
+  otutable <- merge(
+    abund,
+    tax,
+    by = 0,
+    all.x = TRUE,
+    all.y = FALSE,
+    sort = FALSE
+  )
+  colnames(otutable)[1] <- "OTU"
+
+  #extract sample_data (metadata)
+  if(!is.null(physeq@sam_data)) {
+    metadata <- data.frame(
+      phyloseq::sample_data(physeq),
+      row.names = phyloseq::sample_names(physeq), 
+      stringsAsFactors = FALSE, 
+      check.names = FALSE
+    )
+
+    #check if any columns match exactly with rownames
+    #if none matched assume row names are sample identifiers
+    samplesCol <- unlist(lapply(metadata, function(x) {
+      identical(x, rownames(metadata))}))
+
+    if(any(samplesCol)) {
+      #error if a column matched and it's not the first
+      if(!samplesCol[[1]])
+        stop("Sample ID's must be in the first column in the sample metadata, please reorder", call. = FALSE)
+    } else {
+      #assume rownames are sample identifiers, merge at the end with name "SampleID"
+      if(any(colnames(metadata) %in% "SampleID"))
+        stop("A column in the sample metadata is already named \"SampleID\" but does not seem to contain sample ID's", call. = FALSE)
+      metadata$SampleID <- rownames(metadata)
+
+      #reorder columns so SampleID is the first
+      metadata <- metadata[, c(which(colnames(metadata) %in% "SampleID"), 1:(ncol(metadata)-1L)), drop = FALSE]
+    }
+  } else
+    metadata <- NULL
+
+  #extract phylogenetic tree, assumed to be of class "phylo"
+  if(!is.null(physeq@phy_tree)) {
+    tree <- phyloseq::phy_tree(physeq)
+  } else
+    tree <- NULL
+
+  #extract OTU DNA sequences, assumed to be of class "XStringSet"
+  if(!is.null(physeq@refseq)) {
+    #convert XStringSet to DNAbin using a temporary file (easiest)
+    fastaTempFile <- tempfile(pattern = "ampvis2_", fileext = ".fa")
+    Biostrings::writeXStringSet(physeq@refseq, filepath = fastaTempFile)
+  } else
+    fastaTempFile <- NULL
+
+  #load as normally with amp_load
+  ampvis2::amp_load(
+    otutable = otutable,
+    metadata = metadata,
+    tree = tree,
+    fasta = fastaTempFile
+  )
+}
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