feature table

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: qSIP2
 Title: qSIP Analysis
-Version: 0.4.5.9003
+Version: 0.4.5.9004
 Authors@R: 
     person("Jeff", "Kimbrel", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "YOUR-ORCID-ID"))

NAMESPACE

@@ -9,7 +9,7 @@ export(gradient_pos_density_validation)
 export(gradient_position_validation)
 export(isotope_validation)
 export(plot_sample_curves)
-export(qsip_abundance_object)
+export(qsip_feature_data)
 export(qsip_sample_data)
 export(qsip_source_data)
 export(remove_isotopolog_label)

R/qsip_feature_data.R

@@ -0,0 +1,75 @@
+#' qSIP feature table class
+#'
+#' A class to hold and validate a feature abundance table
+#'
+#' @slot data A dataframe or tibble
+#' @slot feature_id Column name with unique taxa IDs
+#'
+#' @export
+#'
+#' @keywords object
+
+qsip_feature_data <- S7::new_class(
+  "qsip_feature_data",
+  properties = list(
+    data = S7::class_data.frame,
+    feature_id = S7::class_character,
+    taxonomy = S7::class_data.frame
+    ),
+  constructor = function(data, feature_id, taxonomy = data.frame()) {
+
+    # rename columns to standardized names
+    data = data |>
+      dplyr::select(feature_id = feature_id,
+                    dplyr::everything()) |>
+      dplyr::ungroup()
+
+    S7::new_object(S7::S7_object(),
+                   data = data,
+                   feature_id = feature_id,
+                   taxonomy = taxonomy)
+  },
+  validator = function(self) {
+      if (any(duplicated(self@data['feature_id']))) {
+        message(glue::glue("There appear to be duplicate ids in the {self@id} column"))
+      }
+
+      #qSIP2::abundance_validation(self@data, 'feature_id')
+
+    }
+)
+
+
+
+#' Add a taxonomy table to qSIP abundance data
+#'
+#' @param x An object of `qsip_feature_data` class
+#' @param taxa A taxa table
+#' @param id The column name for the taxa ids that match the ids in the
+#' abundance table
+#'
+#' @export
+#'
+#' @keywords abundance
+
+add_taxonomy <- S7::new_generic("add_taxonomy", "x")
+
+S7::method(add_taxonomy, qsip_feature_data) <- function(x, taxa, feature_id) {
+
+  x_ids = x@data |> dplyr::pull(feature_id)
+  taxa_ids = taxa |> dplyr::pull(feature_id)
+
+  if (length(setdiff(x_ids, taxa_ids)) > 0) {
+    stop("some ids found in the abundance object are not found in the taxa table")
+  } else if (length(setdiff(taxa_ids, x_ids)) > 0) {
+    setdiff(taxa_ids, x_ids)
+    stop("some ids found in the taxa table are not found in the abundance object")
+  } else {
+
+    # rename taxa id column to the object level ID
+    x@taxonomy = taxa |>
+      dplyr::rename("feature_id" := feature_id)
+
+    x
+  }
+}