restructure output of phylotax()

Author: brendanf

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: phylotax
 Type: Package
 Title: Refine taxonomic assignment of environmental sequences using a taxonomic tree
-Version: 0.0.2.1
+Version: 0.0.3
 Authors@R: person(given = "Brendan", family = "Furneaux",
                   email = "[email protected]",
                   role = c("aut", "cre"))

NEWS.md

@@ -1,3 +1,20 @@
+# phlotax 0.0.3
+
+* **BREAKING CHANGE** `phylotax` returns taxonomic tables in four categories;
+  * "`tip_taxa`" is the assignments which PHYLOTAX has made itself.
+  * "`rejected`" are primary assignments which PHYLOTAX has rejected.
+  * "`retained`" are primary assignments which PHYLOTAX has not rejected;
+    however some of them may still be ambiguous.
+  * "`missing`" are primary assignments whose labels are not present in the
+    tree, so PHYLOTAX has not done anything with them. (But note that this will
+    be empty if no tree was given).
+* `phylotax()` now returns an S3 object of class "`phylotax`".  This should not
+  break anything, and it allows the possibility of nice improvements in the
+  future.
+* `phylotax()$node_taxa` now includes a "`label`" column, and populates it with
+  node labels if they exist, or just the numbers if they don't.  Node labels are
+  also used in trace output.
+
 # phylotax 0.0.2.1
 
 * Two quick bugfix, applying to errors in `taxonomy_sintax()` and

R/taxonomy.R

@@ -541,46 +541,54 @@ new_phylotax_env <- function(tree, taxa, parent = parent.frame()) {
     .parent = parent,
     node_taxa = tibble::tibble(
       node = integer(),
+      label = NULL,
       rank = taxa$rank[FALSE],
       taxon = character()
     ),
-    tip_taxa = dplyr::filter(taxa, .data$label %in% tree$tip.label),
+    tip_taxa = dplyr::filter(taxa, FALSE),
+    retained = dplyr::filter(taxa, .data$label %in% tree$tip.label),
+    rejected = dplyr::filter(taxa, FALSE),
+    missing = dplyr::filter(taxa, !.data$label %in% tree$tip.label),
     tree = tree
   )
 }
 
 
 phylotax_ <- function(tree, taxa, node, ranks, method, e) {
   if (length(ranks) == 0) return()
-
+  nodelabel <- if (!is.null(tree$node.label)) {
+    tree$node.label[node - ape::Ntip(tree)]
+  } else {
+    as.character(node)
+  }
   parents <- phangorn::Ancestors(tree, node, type = "all")
   for (r in ranks) {
     if (is.ordered(ranks)) r <- ordered(r, levels = levels(ranks))
     if (any(e$node_taxa$node %in% parents & e$node_taxa$rank == r)) next
-    taxon <- clade_taxon(tree, e$tip_taxa, node, r)
+    taxon <- clade_taxon(tree, e$retained, node, r)
     if (is.na(taxon)) {
-      futile.logger::flog.debug("Could not assign a %s to node %d.", r, node)
+      futile.logger::flog.debug("Could not assign a %s to node %s.", r, nodelabel)
       for (n in phangorn::Children(tree, node)) {
-          phylotax_(tree, e$tip_taxa, n, ranks, method, e)
+          phylotax_(tree, e$retained, n, ranks, method, e)
       }
       break
     } else {
       children <- phangorn::Children(tree, node)
       if (length(children) > 0) {
         futile.logger::flog.info(
-          "Assigned node %d and its %d children to %s %s.",
-          node, length(children), as.character(r), taxon)
+          "Assigned node %s and its %d children to %s %s.",
+          nodelabel, length(children), as.character(r), taxon)
       } else {
-        futile.logger::flog.info("Assigned node %d to %s %s.", node,
+        futile.logger::flog.info("Assigned node %s to %s %s.", nodelabel,
                                  as.character(r), taxon)
       }
       ranks <- ranks[-1]
       e$node_taxa <- dplyr::bind_rows(
         e$node_taxa,
-        tibble::tibble(node = node, rank = r, taxon = taxon)
+        tibble::tibble(node = node, label = nodelabel, rank = r, taxon = taxon)
       )
       tips <- tree$tip.label[phangorn::Descendants(tree, node, type = "tips")[[1]]]
-      wrongTaxa <- e$tip_taxa %>%
+      wrongTaxa <- e$retained %>%
         dplyr::filter(
           .data$label %in% tips,
           .data$rank == r,
@@ -596,11 +604,16 @@ phylotax_ <- function(tree, taxa, node, ranks, method, e) {
         newAssign[[n]] <- unname(method[n])
       }
       # remove assignments which are not consistent with the one we just chose
-      e$tip_taxa <- dplyr::bind_rows(
-        dplyr::filter(e$tip_taxa, .data$rank < r),
-        dplyr::filter(e$tip_taxa, .data$rank >= r) %>%
-          dplyr::anti_join(wrongTaxa, by = names(wrongTaxa)),
-        newAssign
+      e$tip_taxa <- dplyr::bind_rows(e$tip_taxa, newAssign)
+      e$rejected <- dplyr::bind_rows(
+        e$rejected,
+        dplyr::filter(e$retained, .data$rank >= r) %>%
+          dplyr::semi_join(wrongTaxa, by = names(wrongTaxa))
+      )
+      e$retained <- dplyr::bind_rows(
+        dplyr::filter(e$retained, .data$rank < r),
+        dplyr::filter(e$retained, .data$rank >= r) %>%
+          dplyr::anti_join(wrongTaxa, by = names(wrongTaxa))
       )
     }
   }
@@ -647,14 +660,20 @@ phylotax_ <- function(tree, taxa, node, ranks, method, e) {
 #'   treat each unique combination of values in these columns as a distinct
 #'   method.
 #'
-#' @return a list with two elements, "tip_taxa" and "node_taxa". "tip_taxa" is
-#' a `tibble::tibble()` with the same format as `taxa`, in
-#' which assignments which are inconsistent with the phylogeny have been
-#' removed, and new assignments deduced or confirmed from the phylogeny.
-#' These are identified by the value "phylotax" in the "method" column,
-#' which is created if it does not already exist.  "node_taxa" has columns
-#' "node", "rank" and "taxon", giving taxonomic assignments for the nodes of
-#' the tree.
+#' @return an S3 object with class "`phylotax`", with five elements:
+#' * "`tip_taxa` a `tibble::tibble()` with the same format as `taxa`, containing
+#'   taxonomy assignments made by PHYLOTAX to tips.
+#' * "`node_taxa`" a `tibble::tibble()` with columns "`node`", "`label`",
+#'   "`rank`" and "`taxon`" giving taxonomy assignments made by PHYLOTAX to
+#'   internal nodes.
+#' * "`rejected`" a `tibble::tibble()` with the same format as `taxa` giving
+#'   primary assignments which have been rejected by PHYLOTAX.
+#' * "`retained`" a `tibble::tibble()` with the same format as `taxa` giving
+#'   primary assignments which have not been rehected by PHYLOTAX. These may
+#'   contain inconsistencies that PHYLOTAX was unable to resolve.
+#' * "`missing`" a `tibble::tibble()` with the same format as `taxa`, giving the
+#'   primary assignments which have not been assessed by PHULOTAX because they
+#'   have labels which are not present on the tree.
 #'
 #' @export
 phylotax <- function(
@@ -670,9 +689,13 @@ phylotax <- function(
   e <- new_phylotax_env(tree, count_assignments(taxa), ranks)
   ranks <- sort(unique(taxa$rank))
   phylotax_(tree, taxa, phangorn::getRoot(tree), ranks, method, e)
-  e$tip_taxa$n_tot <- NULL
-  e$tip_taxa$n_diff <- NULL
-  as.list(e)
+  for (member in c("missing", "retained", "rejected", "tip_taxa"))
+    for (n in c("n_tot", "n_diff"))
+      e[[member]][[n]] <- NULL
+  structure(
+    as.list(e),
+    class = "phylotax"
+  )
 }
 
 #' Simple phylogenetic tree for use in examples

README.Rmd

@@ -76,13 +76,24 @@ supports it.
 phylotax_out <- phylotax(tree = example_tree(), taxa = example_taxa())
 ```
 
-PHYLOTAX returns a list containing the tree, taxa assigned to tips,
-and taxa assigned to nodes. Let's look at the tip taxa assignments.
+PHYLOTAX returns a list of class "`phylotax`" containing the tree,
+taxa assignments for tips and internal nodes, as well as tables dividing the
+primary assignments into those which were rejected, those which were retained,
+and those which were missing from the input tree.
 
 ```{r}
 phylotax_out$tip_taxa
 ```
 
+```{r}
+phylotax_out$retained
+```
+
+```{r}
+phylotax_out$rejected
+```
+
+
 Phylotax has used the following logic:
 
 1. It's not possible to decide what the root (node 1) is, because one of its

README.md

@@ -1,7 +1,8 @@
 
 <!-- README.md is generated from README.Rmd. Please edit that file -->
 
-# phylotax
+phylotax
+========
 
 <!-- badges: start -->
 
@@ -11,7 +12,8 @@ status](https://travis-ci.com/brendanf/phylotax.svg?branch=master)](https://trav
 coverage](https://codecov.io/gh/brendanf/phylotax/branch/master/graph/badge.svg)](https://codecov.io/gh/brendanf/phylotax?branch=master)
 <!-- badges: end -->
 
-## Installation
+Installation
+------------
 
 Install the development version from [GitHub](https://github.com/) with:
 
@@ -20,7 +22,8 @@ Install the development version from [GitHub](https://github.com/) with:
 devtools::install_github("brendanf/phylotax")
 ```
 
-## Usage
+Usage
+-----
 
 The PHYLOTAX algorithm takes as input taxonomic annotations from one or
 more primary taxonomic assignment algoirthms, and refines them using a
@@ -40,15 +43,14 @@ plot(example_tree(), show.node.label = TRUE)
 
 And here is a set of taxonomic assignments for the tips of the tree,
 based on two hypothetical primary assignment algorithms “XTAX” and
-“YTAX”. Some of the tips have been assigned to two genera: “Tax1”
-and “Tax2”. The `phylotax` package includes the function `taxtable()`
-which can generate a table of this type based on the output of various
-primary assignment algorithms, but all that’s important is that it
-contains the columns “label”, “rank”, and “taxon”. The ranks need to be
-one of “rootrank”, “domain”, “kingdom”, “phylum”, “class”, “order”,
-“family”, “genus”, and “species”. Our example also has a “method”
-column, which PHYLOTAX uses to identify which assignments come from the
-same source.
+“YTAX”. Some of the tips have been assigned to two genera: “Tax1” and
+“Tax2”. The `phylotax` package includes the function `taxtable()` which
+can generate a table of this type based on the output of various primary
+assignment algorithms, but all that’s important is that it contains the
+columns “label”, “rank”, and “taxon”. The ranks need to be one of
+“rootrank”, “domain”, “kingdom”, “phylum”, “class”, “order”, “family”,
+“genus”, and “species”. Our example also has a “method” column, which
+PHYLOTAX uses to identify which assignments come from the same source.
 
 ``` r
 example_taxa()
@@ -87,28 +89,46 @@ tree supports it.
 
 ``` r
 phylotax_out <- phylotax(tree = example_tree(), taxa = example_taxa())
-#> INFO [2020-10-14 17:35:34] Assigned node 9 and its 2 children to genus Tax2.
-#> INFO [2020-10-14 17:35:34] Assigned node 10 and its 2 children to genus Tax1.
+#> INFO [2020-10-15 15:02:50] Assigned node 3 and its 2 children to genus Tax2.
+#> INFO [2020-10-15 15:02:50] Assigned node 4 and its 2 children to genus Tax1.
 ```
 
-PHYLOTAX returns a list containing the tree, taxa assigned to tips, and
-taxa assigned to nodes. Let’s look at the tip taxa assignments.
+PHYLOTAX returns a list of class “`phylotax`” containing the tree, taxa
+assignments for tips and internal nodes, as well as tables dividing the
+primary assignments into those which were rejected, those which were
+retained, and those which were missing from the input tree.
 
 ``` r
 phylotax_out$tip_taxa
-#> # A tibble: 10 x 4
-#>    label method   rank  taxon
-#>    <chr> <chr>    <ord> <chr>
-#>  1 C     XTAX     genus Tax2 
-#>  2 B     YTAX     genus Tax2 
-#>  3 C     YTAX     genus Tax2 
-#>  4 D     YTAX     genus Tax1 
-#>  5 F     YTAX     genus Tax1 
-#>  6 B     PHYLOTAX genus Tax2 
-#>  7 C     PHYLOTAX genus Tax2 
-#>  8 E     PHYLOTAX genus Tax1 
-#>  9 F     PHYLOTAX genus Tax1 
-#> 10 D     PHYLOTAX genus Tax1
+#> # A tibble: 5 x 4
+#>   label method   rank  taxon
+#>   <chr> <chr>    <ord> <chr>
+#> 1 B     PHYLOTAX genus Tax2 
+#> 2 C     PHYLOTAX genus Tax2 
+#> 3 E     PHYLOTAX genus Tax1 
+#> 4 F     PHYLOTAX genus Tax1 
+#> 5 D     PHYLOTAX genus Tax1
+```
+
+``` r
+phylotax_out$retained
+#> # A tibble: 5 x 4
+#>   label method rank  taxon
+#>   <chr> <chr>  <ord> <chr>
+#> 1 C     XTAX   genus Tax2 
+#> 2 B     YTAX   genus Tax2 
+#> 3 C     YTAX   genus Tax2 
+#> 4 D     YTAX   genus Tax1 
+#> 5 F     YTAX   genus Tax1
+```
+
+``` r
+phylotax_out$rejected
+#> # A tibble: 2 x 4
+#>   label method rank  taxon
+#>   <chr> <chr>  <ord> <chr>
+#> 1 B     XTAX   genus Tax1 
+#> 2 D     XTAX   genus Tax2
 ```
 
 Phylotax has used the following logic:

man/figures/README-unnamed-chunk-2-1.png

@@ -0,0 +1,9 @@
+consensus_test <- tibble::tribble(
+  ~label, ~method, ~rank, ~taxon,
+  "A",    "XTAX",  "genus", "G1",
+  "A",    "XTAX",  "species", "G1 s1",
+  "A",    "YTAX",  "genus", "G2")
+
+test_that("consensus is not assumed for lower taxa when higher taxa are inconsistent", {
+  expect_equal(length(phylotax(taxa = consensus_test)$tip_taxa$method), 0)
+})

man/phylotax.Rd

@@ -1,3 +1,8 @@
+phylotax_out <- phylotax(tree = example_tree(), taxa = example_taxa())
+
 test_that("phylotax does not revert", {
-  expect_known_value(phylotax(tree = example_tree(), taxa = example_taxa()), "phylotax.rds", update = FALSE)
+  expect_known_value(phylotax_out$rejected, "rejected.rds", update = FALSE)
+  expect_known_value(phylotax_out$retained, "retained.rds", update = FALSE)
+  expect_known_value(phylotax_out$tip_taxa, "tip_taxa.rds", update = FALSE)
+  expect_known_value(phylotax_out$node_taxa, "node_taxa.rds", update = FALSE)
 })