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Merged
rmflight merged 2 commits into from
Sep 6, 2025
Merged

Json fix #51

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a5bafe9
- makes sure to set the auto_unbox to FALSE in the toJSON function so…
rmflight Sep 2, 2025
2d91ae2
- adds a check that exporting the single case reads back in and has i…
rmflight Sep 4, 2025
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2 changes: 1 addition & 1 deletion DESCRIPTION
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Original file line number Diff line number Diff line change
@@ -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(
Expand Down
219 changes: 132 additions & 87 deletions R/managing_annotations.R
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Original file line number Diff line number Diff line change
@@ -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
Expand All @@ -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!)
Expand All @@ -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
Expand All @@ -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)
Expand All @@ -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 {
Expand All @@ -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)
}
Expand All @@ -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
}
5 changes: 4 additions & 1 deletion exec/feature_files_2_json.R
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Original file line number Diff line number Diff line change
Expand Up @@ -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
)
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