Merge pull request #51 from MoseleyBioinformaticsLab/json_fix

Json fix

Author: rmflight

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: categoryCompare2
-Version: 0.200.3
+Version: 0.200.4
 Title: Meta-Analysis of High-Throughput Experiments Using Feature
         Annotations
 Authors@R: c(

R/managing_annotations.R

@@ -1,19 +1,19 @@
 #' orgdb annotations
-#' 
+#'
 #' Generate an annotation object for genes based on an "org.*.db" object, and pulling
 #' information from it.
-#' 
+#'
 #' @param orgdb the name of the org.*.db object
 #' @param features which features to get annotations for
 #' @param feature_type which type of IDs to map (see details)
 #' @param annotation_type the type of annotation to grab (see details)
-#' 
+#'
 #' @md
-#' 
+#'
 #' @details This function generates a `categoryCompare2` annotation object
 #' from a Bioconductor "org.*.db" object. Even though different gene identifiers can
 #' be used, almost all of the mappings are via ENTREZID.
-#' 
+#'
 #' The set of feature or gene keys that can be used to create the annotations include:
 #' * ENTREZID: ENTREZ gene ids
 #' * ACCNUM: genbank accession numbers
@@ -25,7 +25,7 @@
 #' * REFSEQ: reference sequence IDs, NM, NP, NR, XP, etc
 #' * UNIGENE: gene ids from UNIPROT eg Hs.88556
 #' * UNIPROT: protein ids from UNIPROT eg P80404
-#' 
+#'
 #' The set of annotations that can be mapped to features include:
 #' * GO: annotations from gene ontology
 #' * PATH: KEGG Pathway identifiers (not updated since 2011!)
@@ -35,54 +35,72 @@
 #' * PROSITE
 #' * PFAM: protein family identifiers
 #' * IPI: protein-protein interactions
-#' 
+#'
 #' For GO annotations, it is also possible to pass `GO` to use all 3 sub-ontologies simultaneously,
 #' or any combination of `BP`, `MF`, and `CC`.
-#' 
+#'
 #' @export
 #' @return annotation object
-#' 
-get_db_annotation <- function(orgdb = "org.Hs.eg.db", features = NULL, feature_type = "ENTREZID",
-                              annotation_type = "GO"){
+#'
+get_db_annotation <- function(
+  orgdb = "org.Hs.eg.db",
+  features = NULL,
+  feature_type = "ENTREZID",
+  annotation_type = "GO"
+) {
   go_types <- c("GO", "BP", "MF", "CC")
   go_sub <- c("BP", "MF", "CC")
   check_package_installed(orgdb)
   suppressPackageStartupMessages(library(orgdb, character.only = TRUE))
-  
+
   annotation_src <- eval(parse(text = orgdb))
   annotation_columns <- AnnotationDbi::columns(annotation_src)
   annotation_keytypes <- AnnotationDbi::keytypes(annotation_src)
-    
+
   if (!(annotation_type %in% c(go_types, annotation_columns))) {
     stop("Unknown annotation type!")
   }
-    
+
   if (!(feature_type %in% annotation_keytypes)) {
     stop("Unknown feature_type!")
   }
-  
+
   if (is.null(features)) {
     features <- AnnotationDbi::keys(annotation_src, feature_type)
   }
-  
+
   if (annotation_type %in% go_types) {
     check_package_installed("GO.db")
     requireNamespace("GO.db")
     godb = GO.db::GO.db
-    feature_ann_map <- suppressMessages(AnnotationDbi::select(annotation_src, keys = features,
-                                                           keytype = feature_type,
-                                                           columns = "GOALL"))
-    
+    feature_ann_map <- suppressMessages(AnnotationDbi::select(
+      annotation_src,
+      keys = features,
+      keytype = feature_type,
+      columns = "GOALL"
+    ))
+
     if (annotation_type %in% go_sub) {
-      feature_ann_map <- feature_ann_map[feature_ann_map$ONTOLOGYALL %in% annotation_type, ]
+      feature_ann_map <- feature_ann_map[
+        feature_ann_map$ONTOLOGYALL %in% annotation_type,
+      ]
     }
-    
-    
-    ann_feature_list <- split(feature_ann_map[[feature_type]], feature_ann_map[["GOALL"]])
+
+    ann_feature_list <- split(
+      feature_ann_map[[feature_type]],
+      feature_ann_map[["GOALL"]]
+    )
     ann_feature_list <- lapply(ann_feature_list, unique)
-    ann_description <- suppressMessages(AnnotationDbi::select(godb, keys = names(ann_feature_list), columns = "TERM", keytype = "GOID")$TERM)
+    ann_description <- suppressMessages(
+      AnnotationDbi::select(
+        godb,
+        keys = names(ann_feature_list),
+        columns = "TERM",
+        keytype = "GOID"
+      )$TERM
+    )
     names(ann_description) <- names(ann_feature_list)
-    
+
     if (annotation_type %in% "GO") {
       go_ontology_map <- unique(feature_ann_map[, c("GOALL", "ONTOLOGYALL")])
       go_ontology <- go_ontology_map$ONTOLOGYALL
@@ -91,42 +109,51 @@ get_db_annotation <- function(orgdb = "org.Hs.eg.db", features = NULL, feature_t
       ann_description <- paste0(go_ontology, ":", ann_description)
       names(ann_description) <- names(go_ontology)
     }
-    
-    
-    annotation_obj <- categoryCompare2::annotation(annotation_features = ann_feature_list,
-                                                   description = ann_description,
-                                                   annotation_type = annotation_type,
-                                                   feature_type = feature_type)
+
+    annotation_obj <- categoryCompare2::annotation(
+      annotation_features = ann_feature_list,
+      description = ann_description,
+      annotation_type = annotation_type,
+      feature_type = feature_type
+    )
   } else {
-    feature_ann_map <- suppressMessages(AnnotationDbi::select(annotation_src, keys = features,
-                                                              keytype = feature_type,
-                                                              columns = annotation_type))
-    ann_feature_list <- split(feature_ann_map[[feature_type]], feature_ann_map[[annotation_type]])
+    feature_ann_map <- suppressMessages(AnnotationDbi::select(
+      annotation_src,
+      keys = features,
+      keytype = feature_type,
+      columns = annotation_type
+    ))
+    ann_feature_list <- split(
+      feature_ann_map[[feature_type]],
+      feature_ann_map[[annotation_type]]
+    )
     ann_feature_list <- lapply(ann_feature_list, unique)
-    
-    annotation_obj <- categoryCompare2::annotation(annotation_features = ann_feature_list,
-                                                   annotation_type = annotation_type,
-                                                   feature_type = feature_type)
+
+    annotation_obj <- categoryCompare2::annotation(
+      annotation_features = ann_feature_list,
+      annotation_type = annotation_type,
+      feature_type = feature_type
+    )
   }
-  
+
   annotation_obj
 }
 
 
 #' annotation to json
-#' 
+#'
 #' Given a `categoryCompare2` annotation object, generate a JSON representation
 #' that can be used with the command line executable
-#' 
+#'
 #' @param annotation_obj the annotation object
 #' @param json_file the file to save it to
-#' 
+#'
 #' @return the json string (invisibly)
 #' @export
-annotation_2_json <- function(annotation_obj, json_file = NULL){
-  obj_list <- purrr::map(slotNames(annotation_obj), function(x){
+annotation_2_json <- function(annotation_obj, json_file = NULL) {
+  obj_list <- purrr::map(slotNames(annotation_obj), function(x) {
     tmp_data <- slot(annotation_obj, x)
-    
+
     if (length(tmp_data) != 0) {
       if (x %in% c("description", "links")) {
         out_data <- as.list(tmp_data)
@@ -139,17 +166,17 @@ annotation_2_json <- function(annotation_obj, json_file = NULL){
     out_data
   })
   names(obj_list) <- slotNames(annotation_obj)
-  
+
   obj_list <- obj_list[!purrr::map_lgl(obj_list, is.null)]
-  
-  obj_json <- jsonlite::toJSON(obj_list, pretty = TRUE, auto_unbox = TRUE)
+
+  obj_json <- jsonlite::toJSON(obj_list, pretty = TRUE, auto_unbox = FALSE)
   if (!is.null(json_file)) {
     cat(obj_json, file = json_file, sep = "\n")
-  } 
+  }
   invisible(obj_json)
 }
 
-replace_null <- function(x){
+replace_null <- function(x) {
   if (is.null(x)) {
     NA
   } else {
@@ -158,26 +185,32 @@ replace_null <- function(x){
 }
 
 #' json to annotation
-#' 
+#'
 #' Given a JSON based annotation object, read it in and create the `annotation`
-#' for actually doing enrichment. 
-#' 
+#' for actually doing enrichment.
+#'
 #' @param json_file the json annotation file
-#' 
+#'
 #' @return annotation object
 #' @export
-json_2_annotation <- function(json_file){
+json_2_annotation <- function(json_file) {
   stopifnot(file.exists(json_file))
   annotation_list <- jsonlite::fromJSON(json_file, simplifyVector = TRUE)
   #print(names(annotation_list))
-  
+
   if (is.null(names(annotation_list))) {
     annotation_list <- annotation_list[[1]]
   }
-  
+
   if (!is.null(annotation_list$description)) {
-    annotation_list$description <- purrr::map(annotation_list$description, replace_null)
-    annotation_list$description <- unlist(annotation_list$description, use.names = TRUE)
+    annotation_list$description <- purrr::map(
+      annotation_list$description,
+      replace_null
+    )
+    annotation_list$description <- unlist(
+      annotation_list$description,
+      use.names = TRUE
+    )
   } else {
     annotation_list$description <- character(0)
   }
@@ -189,65 +222,77 @@ json_2_annotation <- function(json_file){
 
   #print(names(annotation_list))
   #print(annotation_list$description)
-  annotation(annotation_features = annotation_list$annotation_features,
-             annotation_type = annotation_list$annotation_type,
-             description = annotation_list$description,
-             links = annotation_list$links,
-             feature_type = annotation_list$feature_type)
+  annotation(
+    annotation_features = annotation_list$annotation_features,
+    annotation_type = annotation_list$annotation_type,
+    description = annotation_list$description,
+    links = annotation_list$links,
+    feature_type = annotation_list$feature_type
+  )
 }
 
 #' annotation reversal
-#' 
+#'
 #' Given a JSON file of features to annotations, reverse to turn it into
 #' annotations to features, and optionally add some meta-information about them.
-#' 
+#'
 #' @param json_file the json file to use
 #' @param out_file the json file to write out to
 #' @param feature_type the type of features
 #' @param annotation_type the type of annotations
-#' 
+#'
 #' @importFrom jsonlite fromJSON toJSON
 #' @export
 #' @return the json object, invisibly
-#' 
-json_annotation_reversal <- function(json_file, out_file = "annotations.json",
-                                feature_type = NULL, annotation_type = NULL){
+#'
+json_annotation_reversal <- function(
+  json_file,
+  out_file = "annotations.json",
+  feature_type = NULL,
+  annotation_type = NULL
+) {
   stopifnot(file.exists(json_file))
-  
-  in_annotation <- jsonlite::fromJSON(json_file, simplifyVector = FALSE, flatten = TRUE)
+
+  in_annotation <- jsonlite::fromJSON(
+    json_file,
+    simplifyVector = FALSE,
+    flatten = TRUE
+  )
   if (length(in_annotation) == 1) {
     in_annotation <- in_annotation[[1]]
   }
-  
+
   if (!is.null(in_annotation$Annotations)) {
     gene_annotations <- in_annotation$Annotations
   } else {
     gene_annotations <- in_annotation # we assume that if there is no Annotation
-                                      # specific entry, then it is probably just the
-                                      # gene annotations, and grab them all.
+    # specific entry, then it is probably just the
+    # gene annotations, and grab them all.
   }
-  
+
   if (!is.null(in_annotation$Description)) {
     annotation_description <- in_annotation$Description
     if (is.list(annotation_description)) {
       annotation_description <- unlist(annotation_description, use.names = TRUE)
     } else {
       warning("Description must be a named list! Removing Descriptions!")
       annotation_description <- character(0)
-    } 
+    }
   } else {
     annotation_description <- character(0)
   }
-  
+
   rev_annotation <- Biobase::reverseSplit(gene_annotations)
   rev_annotation <- purrr::map(rev_annotation, unique)
-  
-  out_annotation <- annotation(annotation_features = rev_annotation,
-                               description = annotation_description,
-                               links = character(0),
-                               annotation_type = annotation_type,
-                               feature_type = feature_type)
-  
+
+  out_annotation <- annotation(
+    annotation_features = rev_annotation,
+    description = annotation_description,
+    links = character(0),
+    annotation_type = annotation_type,
+    feature_type = feature_type
+  )
+
   out_json <- annotation_2_json(out_annotation, out_file)
   out_json
 }

exec/feature_files_2_json.R

@@ -128,4 +128,7 @@ if (!("universe" %in% names(file_args))) {
   feature_lists <- get_significant_feature_lists(file_args)
 }
 
-cat(jsonlite::toJSON(feature_lists, pretty = TRUE), file = script_options$json)
+cat(
+  jsonlite::toJSON(feature_lists, pretty = TRUE, auto_unbox = FALSE),
+  file = script_options$json
+)