From e351d2fc0fd5c5d3de4f64dd4b77df349b317421 Mon Sep 17 00:00:00 2001 From: Danielle Callan Date: Tue, 18 Nov 2025 09:39:00 -0500 Subject: [PATCH 1/7] try to get everything on same veupathutils as computations package is --- DESCRIPTION | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 74568de..03d54c8 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: MicrobiomeDB Title: Curated Data and Analysis Tools from MicrobiomeDB.org -Version: 1.1.1 +Version: 1.1.3 Authors@R: c(person(given = "Danielle", family = "Callan", @@ -12,15 +12,15 @@ Imports: data.table, DESeq2, igraph, - veupathUtils, + veupathUtils (>= 2.7.0), Maaslin2, methods, - microbiomeComputations, + microbiomeComputations (>= 5.1.6), purrr, SummarizedExperiment, TreeSummarizedExperiment Remotes: - microbiomeDB/veupathUtils, + VEuPathDB/veupathUtils, microbiomeDB/corGraph, microbiomeDB/microbiomeComputations, microbiomeDB/microbiomeData From c3fa07de23ab18798a37a60696b40921e948138d Mon Sep 17 00:00:00 2001 From: Danielle Callan Date: Tue, 18 Nov 2025 10:52:30 -0500 Subject: [PATCH 2/7] attempt 1 fix maaslin dep --- DESCRIPTION | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 03d54c8..6b44168 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -23,7 +23,8 @@ Remotes: VEuPathDB/veupathUtils, microbiomeDB/corGraph, microbiomeDB/microbiomeComputations, - microbiomeDB/microbiomeData + microbiomeDB/microbiomeData, + bioc::Maaslin2 URL: https://github.com/microbiomeDB/MicrobiomeDB, https://microbiomedb.github.io/MicrobiomeDB/ BugReports: https://github.com/microbiomeDB/MicrobiomeDB/issues Description: This package is intended to be used to explore the curated datasets from MicrobiomeDB.org, as well as your own datasets. It comes pre-packaged with the same functions used to power the analysis tools from the website. It also contains functions to facilitate easily transforming data between our custom objects, phyloseq objects, and .biom files that you can upload to the website. From 315b9b79f84d8eb7ae6c48d5cbc89d5b31c1d556 Mon Sep 17 00:00:00 2001 From: Danielle Callan Date: Fri, 21 Nov 2025 12:01:01 -0500 Subject: [PATCH 3/7] veupathUtils -> mbioUtils --- R/class-MbioDataset.R | 2 +- R/constructors-MbioDataset.R | 136 +++++++++++++-------------- R/importers-MbioDataset.R | 12 +-- R/method-differentialAbundance.R | 46 ++++----- R/methods-ComputeResult.R | 26 ++--- R/methods-MbioDataset.R | 40 ++++---- R/reexports-microbiomeComputations.R | 10 +- 7 files changed, 136 insertions(+), 136 deletions(-) diff --git a/R/class-MbioDataset.R b/R/class-MbioDataset.R index bb745a1..ebfca3c 100644 --- a/R/class-MbioDataset.R +++ b/R/class-MbioDataset.R @@ -22,7 +22,7 @@ check_mbio_dataset <- function(object) { #' This class represents a MicrobiomeDB dataset. #' @name MbioDataset-class #' @rdname MbioDataset-class -#' @importFrom veupathUtils SampleMetadata +#' @importFrom mbioUtils SampleMetadata setClass("MbioDataset", slots = c( collections = "Collections", diff --git a/R/constructors-MbioDataset.R b/R/constructors-MbioDataset.R index 8f78df8..0a30ab4 100644 --- a/R/constructors-MbioDataset.R +++ b/R/constructors-MbioDataset.R @@ -1,13 +1,13 @@ -#' @importFrom veupathUtils findRecordIdColumn -#' @importFrom veupathUtils findAncestorIdColumns -#' @importFrom veupathUtils getDataFromSource +#' @importFrom mbioUtils findRecordIdColumn +#' @importFrom mbioUtils findAncestorIdColumns +#' @importFrom mbioUtils getDataFromSource sampleMetadataBuilder <- function(dataSource) { - dt <- veupathUtils::getDataFromSource(dataSource, keepIdsAndNumbersOnly=FALSE, cleanColumnNames=TRUE) + dt <- mbioUtils::getDataFromSource(dataSource, keepIdsAndNumbersOnly=FALSE, cleanColumnNames=TRUE) dataColNames <- names(dt) - recordIdColumn <- veupathUtils::findRecordIdColumn(dataColNames) - ancestorIdColumns <- veupathUtils::findAncestorIdColumns(dataColNames) + recordIdColumn <- mbioUtils::findRecordIdColumn(dataColNames) + ancestorIdColumns <- mbioUtils::findAncestorIdColumns(dataColNames) sampleMetadata <- new("SampleMetadata", data=dt, @@ -54,8 +54,8 @@ sampleMetadataFromDataSources <- function(dataSources) { #' @param ontology An data.frame containing the ontology of the dataset, or a character vector #' containing a file path to a data.frame #' @export -#' @importFrom veupathUtils Collection -#' @importFrom veupathUtils Collections +#' @importFrom mbioUtils Collection +#' @importFrom mbioUtils Collections #' @rdname MbioDataset-methods setGeneric("MbioDataset", function(collections, metadata, ontology) standardGeneric("MbioDataset")) @@ -168,369 +168,369 @@ setMethod("MbioDataset", signature("Collections", "character", "character"), fun #' @rdname MbioDataset-methods #' @aliases MbioDataset,Collection,SampleMetadata,missing-method setMethod("MbioDataset", signature("Collection", "SampleMetadata", "missing"), function(collections, metadata, ontology) { - new("MbioDataset", collections = veupathUtils::Collections(collections), metadata = metadata) + new("MbioDataset", collections = mbioUtils::Collections(collections), metadata = metadata) }) #' @rdname MbioDataset-methods #' @aliases MbioDataset,Collection,SampleMetadata,data.frame-method setMethod("MbioDataset", signature("Collection", "SampleMetadata", "data.frame"), function(collections, metadata, ontology) { warning("Ontology specified but not used when a Collection object is provided.") - new("MbioDataset", collections = veupathUtils::Collections(collections), metadata = metadata) + new("MbioDataset", collections = mbioUtils::Collections(collections), metadata = metadata) }) #' @rdname MbioDataset-methods #' @aliases MbioDataset,Collection,SampleMetadata,character-method setMethod("MbioDataset", signature("Collection", "SampleMetadata", "character"), function(collections, metadata, ontology) { warning("Ontology specified but not used when a Collection object is provided.") - new("MbioDataset", collections = veupathUtils::Collections(collections), metadata = metadata) + new("MbioDataset", collections = mbioUtils::Collections(collections), metadata = metadata) }) #' @rdname MbioDataset-methods #' @aliases MbioDataset,Collection,data.frame,missing-method setMethod("MbioDataset", signature("Collection", "data.frame", "missing"), function(collections, metadata, ontology) { - new("MbioDataset", collections = veupathUtils::Collections(collections), metadata = sampleMetadataBuilder(metadata)) + new("MbioDataset", collections = mbioUtils::Collections(collections), metadata = sampleMetadataBuilder(metadata)) }) #' @rdname MbioDataset-methods #' @aliases MbioDataset,Collection,data.frame,data.frame-method setMethod("MbioDataset", signature("Collection", "data.frame", "data.frame"), function(collections, metadata, ontology) { warning("Ontology specified but not used when a Collection object is provided.") - new("MbioDataset", collections = veupathUtils::Collections(collections), metadata = sampleMetadataBuilder(metadata)) + new("MbioDataset", collections = mbioUtils::Collections(collections), metadata = sampleMetadataBuilder(metadata)) }) #' @rdname MbioDataset-methods #' @aliases MbioDataset,Collection,data.frame,character-method setMethod("MbioDataset", signature("Collection", "data.frame", "character"), function(collections, metadata, ontology) { warning("Ontology specified but not used when a Collection object is provided.") - new("MbioDataset", collections = veupathUtils::Collections(collections), metadata = sampleMetadataBuilder(metadata)) + new("MbioDataset", collections = mbioUtils::Collections(collections), metadata = sampleMetadataBuilder(metadata)) }) #' @rdname MbioDataset-methods #' @aliases MbioDataset,Collection,list,missing-method setMethod("MbioDataset", signature("Collection", "list", "missing"), function(collections, metadata, ontology) { - new("MbioDataset", collections = veupathUtils::Collections(collections), metadata = sampleMetadataFromDataSources(metadata)) + new("MbioDataset", collections = mbioUtils::Collections(collections), metadata = sampleMetadataFromDataSources(metadata)) }) #' @rdname MbioDataset-methods #' @aliases MbioDataset,Collection,list,data.frame-method setMethod("MbioDataset", signature("Collection", "list", "data.frame"), function(collections, metadata, ontology) { warning("Ontology specified but not used when a Collection object is provided.") - new("MbioDataset", collections = veupathUtils::Collections(collections), metadata = sampleMetadataFromDataSources(metadata)) + new("MbioDataset", collections = mbioUtils::Collections(collections), metadata = sampleMetadataFromDataSources(metadata)) }) #' @rdname MbioDataset-methods #' @aliases MbioDataset,Collection,list,character-method setMethod("MbioDataset", signature("Collection", "list", "character"), function(collections, metadata, ontology) { warning("Ontology specified but not used when a Collection object is provided.") - new("MbioDataset", collections = veupathUtils::Collections(collections), metadata = sampleMetadataFromDataSources(metadata)) + new("MbioDataset", collections = mbioUtils::Collections(collections), metadata = sampleMetadataFromDataSources(metadata)) }) #' @rdname MbioDataset-methods #' @aliases MbioDataset,Collection,missing,missing-method setMethod("MbioDataset", signature("Collection", "missing", "missing"), function(collections, metadata, ontology) { - new("MbioDataset", collections = veupathUtils::Collections(collections)) + new("MbioDataset", collections = mbioUtils::Collections(collections)) }) #' @rdname MbioDataset-methods #' @aliases MbioDataset,Collection,missing,data.frame-method setMethod("MbioDataset", signature("Collection", "missing", "data.frame"), function(collections, metadata, ontology) { warning("Ontology specified but not used when a Collection object is provided.") - new("MbioDataset", collections = veupathUtils::Collections(collections), metadata = sampleMetadataBuilder(metadata)) + new("MbioDataset", collections = mbioUtils::Collections(collections), metadata = sampleMetadataBuilder(metadata)) }) #' @rdname MbioDataset-methods #' @aliases MbioDataset,Collection,missing,character-method setMethod("MbioDataset", signature("Collection", "missing", "character"), function(collections, metadata, ontology) { warning("Ontology specified but not used when a Collection object is provided.") - new("MbioDataset", collections = veupathUtils::Collections(collections), metadata = sampleMetadataBuilder(metadata)) + new("MbioDataset", collections = mbioUtils::Collections(collections), metadata = sampleMetadataBuilder(metadata)) }) #' @rdname MbioDataset-methods #' @aliases MbioDataset,Collection,character,missing-method setMethod("MbioDataset", signature("Collection", "character", "missing"), function(collections, metadata, ontology) { - new("MbioDataset", collections = veupathUtils::Collections(collections), metadata = sampleMetadataFromDataSources(list(metadata))) + new("MbioDataset", collections = mbioUtils::Collections(collections), metadata = sampleMetadataFromDataSources(list(metadata))) }) #' @rdname MbioDataset-methods #' @aliases MbioDataset,Collection,character,data.frame-method setMethod("MbioDataset", signature("Collection", "character", "data.frame"), function(collections, metadata, ontology) { warning("Ontology specified but not used when a Collection object is provided.") - new("MbioDataset", collections = veupathUtils::Collections(collections), metadata = sampleMetadataBuilder(metadata)) + new("MbioDataset", collections = mbioUtils::Collections(collections), metadata = sampleMetadataBuilder(metadata)) }) #' @rdname MbioDataset-methods #' @aliases MbioDataset,Collection,character,character-method setMethod("MbioDataset", signature("Collection", "character", "character"), function(collections, metadata, ontology) { warning("Ontology specified but not used when a Collection object is provided.") - new("MbioDataset", collections = veupathUtils::Collections(collections), metadata = sampleMetadataBuilder(metadata)) + new("MbioDataset", collections = mbioUtils::Collections(collections), metadata = sampleMetadataBuilder(metadata)) }) #' @rdname MbioDataset-methods #' @aliases MbioDataset,list,SampleMetadata,missing-method setMethod("MbioDataset", signature("list", "SampleMetadata", "missing"), function(collections, metadata, ontology) { - new("MbioDataset", collections = veupathUtils::Collections(collections), metadata = metadata) + new("MbioDataset", collections = mbioUtils::Collections(collections), metadata = metadata) }) #' @rdname MbioDataset-methods #' @aliases MbioDataset,list,SampleMetadata,data.frame-method setMethod("MbioDataset", signature("list", "SampleMetadata", "data.frame"), function(collections, metadata, ontology) { - new("MbioDataset", collections = veupathUtils::Collections(collections, ontology), metadata = metadata) + new("MbioDataset", collections = mbioUtils::Collections(collections, ontology), metadata = metadata) }) #' @rdname MbioDataset-methods #' @aliases MbioDataset,list,SampleMetadata,character-method setMethod("MbioDataset", signature("list", "SampleMetadata", "character"), function(collections, metadata, ontology) { - new("MbioDataset", collections = veupathUtils::Collections(collections, data.table::fread(ontology)), metadata = metadata) + new("MbioDataset", collections = mbioUtils::Collections(collections, data.table::fread(ontology)), metadata = metadata) }) #' @rdname MbioDataset-methods #' @aliases MbioDataset,list,data.frame,missing-method setMethod("MbioDataset", signature("list", "data.frame", "missing"), function(collections, metadata, ontology) { - new("MbioDataset", collections = veupathUtils::Collections(collections), metadata = sampleMetadataBuilder(metadata)) + new("MbioDataset", collections = mbioUtils::Collections(collections), metadata = sampleMetadataBuilder(metadata)) }) #' @rdname MbioDataset-methods #' @aliases MbioDataset,list,data.frame,data.frame-method setMethod("MbioDataset", signature("list", "data.frame", "data.frame"), function(collections, metadata, ontology) { - new("MbioDataset", collections = veupathUtils::Collections(collections, ontology), metadata = sampleMetadataBuilder(metadata)) + new("MbioDataset", collections = mbioUtils::Collections(collections, ontology), metadata = sampleMetadataBuilder(metadata)) }) #' @rdname MbioDataset-methods #' @aliases MbioDataset,list,data.frame,character-method setMethod("MbioDataset", signature("list", "data.frame", "character"), function(collections, metadata, ontology) { - new("MbioDataset", collections = veupathUtils::Collections(collections, data.table::fread(ontology)), metadata = sampleMetadataBuilder(metadata)) + new("MbioDataset", collections = mbioUtils::Collections(collections, data.table::fread(ontology)), metadata = sampleMetadataBuilder(metadata)) }) #' @rdname MbioDataset-methods #' @aliases MbioDataset,list,missing,missing-method setMethod("MbioDataset", signature("list", "missing", "missing"), function(collections, metadata, ontology) { - new("MbioDataset", collections = veupathUtils::Collections(collections)) + new("MbioDataset", collections = mbioUtils::Collections(collections)) }) #' @rdname MbioDataset-methods #' @aliases MbioDataset,list,missing,data.frame-method setMethod("MbioDataset", signature("list", "missing", "data.frame"), function(collections, metadata, ontology) { - new("MbioDataset", collections = veupathUtils::Collections(collections, ontology), metadata = sampleMetadataFromDataSources(metadata)) + new("MbioDataset", collections = mbioUtils::Collections(collections, ontology), metadata = sampleMetadataFromDataSources(metadata)) }) #' @rdname MbioDataset-methods #' @aliases MbioDataset,list,missing,character-method setMethod("MbioDataset", signature("list", "missing", "character"), function(collections, metadata, ontology) { - new("MbioDataset", collections = veupathUtils::Collections(collections, data.table::fread(ontology)), metadata = sampleMetadataFromDataSources(metadata)) + new("MbioDataset", collections = mbioUtils::Collections(collections, data.table::fread(ontology)), metadata = sampleMetadataFromDataSources(metadata)) }) #' @rdname MbioDataset-methods #' @aliases MbioDataset,list,list,missing-method setMethod("MbioDataset", signature("list", "list", "missing"), function(collections, metadata, ontology) { - new("MbioDataset", collections = veupathUtils::Collections(collections), metadata = sampleMetadataFromDataSources(metadata)) + new("MbioDataset", collections = mbioUtils::Collections(collections), metadata = sampleMetadataFromDataSources(metadata)) }) #' @rdname MbioDataset-methods #' @aliases MbioDataset,list,list,data.frame-method setMethod("MbioDataset", signature("list", "list", "data.frame"), function(collections, metadata, ontology) { - new("MbioDataset", collections = veupathUtils::Collections(collections, ontology), metadata = sampleMetadataFromDataSources(metadata)) + new("MbioDataset", collections = mbioUtils::Collections(collections, ontology), metadata = sampleMetadataFromDataSources(metadata)) }) #' @rdname MbioDataset-methods #' @aliases MbioDataset,list,list,character-method setMethod("MbioDataset", signature("list", "list", "character"), function(collections, metadata, ontology) { - new("MbioDataset", collections = veupathUtils::Collections(collections, data.table::fread(ontology)), metadata = sampleMetadataFromDataSources(metadata)) + new("MbioDataset", collections = mbioUtils::Collections(collections, data.table::fread(ontology)), metadata = sampleMetadataFromDataSources(metadata)) }) #' @rdname MbioDataset-methods #' @aliases MbioDataset,list,character,missing-method setMethod("MbioDataset", signature("list", "character", "missing"), function(collections, metadata, ontology) { - new("MbioDataset", collections = veupathUtils::Collections(collections), metadata = sampleMetadataFromDataSources(list(metadata))) + new("MbioDataset", collections = mbioUtils::Collections(collections), metadata = sampleMetadataFromDataSources(list(metadata))) }) #' @rdname MbioDataset-methods #' @aliases MbioDataset,list,character,data.frame-method setMethod("MbioDataset", signature("list", "character", "data.frame"), function(collections, metadata, ontology) { - new("MbioDataset", collections = veupathUtils::Collections(collections, ontology), metadata = sampleMetadataFromDataSources(list(metadata))) + new("MbioDataset", collections = mbioUtils::Collections(collections, ontology), metadata = sampleMetadataFromDataSources(list(metadata))) }) #' @rdname MbioDataset-methods #' @aliases MbioDataset,list,character,character-method setMethod("MbioDataset", signature("list", "character", "character"), function(collections, metadata, ontology) { - new("MbioDataset", collections = veupathUtils::Collections(collections, data.table::fread(ontology)), metadata = sampleMetadataFromDataSources(list(metadata))) + new("MbioDataset", collections = mbioUtils::Collections(collections, data.table::fread(ontology)), metadata = sampleMetadataFromDataSources(list(metadata))) }) #' @rdname MbioDataset-methods #' @aliases MbioDataset,data.frame,SampleMetadata,missing-method setMethod("MbioDataset", signature("data.frame", "SampleMetadata", "missing"), function(collections, metadata, ontology) { - new("MbioDataset", collections = veupathUtils::Collections(collections), metadata = metadata) + new("MbioDataset", collections = mbioUtils::Collections(collections), metadata = metadata) }) #' @rdname MbioDataset-methods #' @aliases MbioDataset,data.frame,SampleMetadata,data.frame-method setMethod("MbioDataset", signature("data.frame", "SampleMetadata", "data.frame"), function(collections, metadata, ontology) { - new("MbioDataset", collections = veupathUtils::Collections(collections, ontology), metadata = metadata) + new("MbioDataset", collections = mbioUtils::Collections(collections, ontology), metadata = metadata) }) #' @rdname MbioDataset-methods #' @aliases MbioDataset,data.frame,SampleMetadata,character-method setMethod("MbioDataset", signature("data.frame", "SampleMetadata", "character"), function(collections, metadata, ontology) { - new("MbioDataset", collections = veupathUtils::Collections(collections, data.table::fread(ontology)), metadata = metadata) + new("MbioDataset", collections = mbioUtils::Collections(collections, data.table::fread(ontology)), metadata = metadata) }) #' @rdname MbioDataset-methods #' @aliases MbioDataset,data.frame,list,missing-method setMethod("MbioDataset", signature("data.frame", "list", "missing"), function(collections, metadata, ontology) { - new("MbioDataset", collections = veupathUtils::Collections(collections), metadata = sampleMetadataFromDataSources(metadata)) + new("MbioDataset", collections = mbioUtils::Collections(collections), metadata = sampleMetadataFromDataSources(metadata)) }) #' @rdname MbioDataset-methods #' @aliases MbioDataset,data.frame,list,data.frame-method setMethod("MbioDataset", signature("data.frame", "list", "data.frame"), function(collections, metadata, ontology) { - new("MbioDataset", collections = veupathUtils::Collections(collections, ontology), metadata = sampleMetadataFromDataSources(metadata)) + new("MbioDataset", collections = mbioUtils::Collections(collections, ontology), metadata = sampleMetadataFromDataSources(metadata)) }) #' @rdname MbioDataset-methods #' @aliases MbioDataset,data.frame,list,character-method setMethod("MbioDataset", signature("data.frame", "list", "character"), function(collections, metadata, ontology) { - new("MbioDataset", collections = veupathUtils::Collections(collections, data.table::fread(ontology)), metadata = sampleMetadataFromDataSources(metadata)) + new("MbioDataset", collections = mbioUtils::Collections(collections, data.table::fread(ontology)), metadata = sampleMetadataFromDataSources(metadata)) }) #' @rdname MbioDataset-methods #' @aliases MbioDataset,data.frame,missing,missing-method setMethod("MbioDataset", signature("data.frame", "missing", "missing"), function(collections, metadata, ontology) { - new("MbioDataset", collections = veupathUtils::Collections(collections)) + new("MbioDataset", collections = mbioUtils::Collections(collections)) }) #' @rdname MbioDataset-methods #' @aliases MbioDataset,data.frame,missing,data.frame-method setMethod("MbioDataset", signature("data.frame", "missing", "data.frame"), function(collections, metadata, ontology) { - new("MbioDataset", collections = veupathUtils::Collections(collections, ontology)) + new("MbioDataset", collections = mbioUtils::Collections(collections, ontology)) }) #' @rdname MbioDataset-methods #' @aliases MbioDataset,data.frame,missing,character-method setMethod("MbioDataset", signature("data.frame", "missing", "character"), function(collections, metadata, ontology) { - new("MbioDataset", collections = veupathUtils::Collections(collections, data.table::fread(ontology))) + new("MbioDataset", collections = mbioUtils::Collections(collections, data.table::fread(ontology))) }) #' @rdname MbioDataset-methods #' @aliases MbioDataset,data.frame,data.frame,missing-method setMethod("MbioDataset", signature("data.frame", "data.frame", "missing"), function(collections, metadata, ontology) { - new("MbioDataset", collections = veupathUtils::Collections(collections), metadata = sampleMetadataBuilder(metadata)) + new("MbioDataset", collections = mbioUtils::Collections(collections), metadata = sampleMetadataBuilder(metadata)) }) #' @rdname MbioDataset-methods #' @aliases MbioDataset,data.frame,data.frame,data.frame-method setMethod("MbioDataset", signature("data.frame", "data.frame", "data.frame"), function(collections, metadata, ontology) { - new("MbioDataset", collections = veupathUtils::Collections(collections, ontology), metadata = sampleMetadataBuilder(metadata)) + new("MbioDataset", collections = mbioUtils::Collections(collections, ontology), metadata = sampleMetadataBuilder(metadata)) }) #' @rdname MbioDataset-methods #' @aliases MbioDataset,data.frame,data.frame,character-method setMethod("MbioDataset", signature("data.frame", "data.frame", "character"), function(collections, metadata, ontology) { - new("MbioDataset", collections = veupathUtils::Collections(collections, data.table::fread(ontology)), metadata = sampleMetadataBuilder(metadata)) + new("MbioDataset", collections = mbioUtils::Collections(collections, data.table::fread(ontology)), metadata = sampleMetadataBuilder(metadata)) }) #' @rdname MbioDataset-methods #' @aliases MbioDataset,data.frame,character,missing-method setMethod("MbioDataset", signature("data.frame", "character", "missing"), function(collections, metadata, ontology) { - new("MbioDataset", collections = veupathUtils::Collections(collections), metadata = sampleMetadataFromDataSources(list(metadata))) + new("MbioDataset", collections = mbioUtils::Collections(collections), metadata = sampleMetadataFromDataSources(list(metadata))) }) #' @rdname MbioDataset-methods #' @aliases MbioDataset,data.frame,character,data.frame-method setMethod("MbioDataset", signature("data.frame", "character", "data.frame"), function(collections, metadata, ontology) { - new("MbioDataset", collections = veupathUtils::Collections(collections, ontology), metadata = sampleMetadataFromDataSources(list(metadata))) + new("MbioDataset", collections = mbioUtils::Collections(collections, ontology), metadata = sampleMetadataFromDataSources(list(metadata))) }) #' @rdname MbioDataset-methods #' @aliases MbioDataset,data.frame,character,character-method setMethod("MbioDataset", signature("data.frame", "character", "character"), function(collections, metadata, ontology) { - new("MbioDataset", collections = veupathUtils::Collections(collections, data.table::fread(ontology)), metadata = sampleMetadataFromDataSources(list(metadata))) + new("MbioDataset", collections = mbioUtils::Collections(collections, data.table::fread(ontology)), metadata = sampleMetadataFromDataSources(list(metadata))) }) #' @rdname MbioDataset-methods #' @aliases MbioDataset,character,character,missing-method setMethod("MbioDataset", signature("character", "character", "missing"), function(collections, metadata, ontology) { - new("MbioDataset", collections = veupathUtils::Collections(collections), metadata = sampleMetadataFromDataSources(list(metadata))) + new("MbioDataset", collections = mbioUtils::Collections(collections), metadata = sampleMetadataFromDataSources(list(metadata))) }) #' @rdname MbioDataset-methods #' @aliases MbioDataset,character,character,data.frame-method setMethod("MbioDataset", signature("character", "character", "data.frame"), function(collections, metadata, ontology) { - new("MbioDataset", collections = veupathUtils::Collections(collections, ontology), metadata = sampleMetadataFromDataSources(list(metadata))) + new("MbioDataset", collections = mbioUtils::Collections(collections, ontology), metadata = sampleMetadataFromDataSources(list(metadata))) }) #' @rdname MbioDataset-methods #' @aliases MbioDataset,character,character,character-method setMethod("MbioDataset", signature("character", "character", "character"), function(collections, metadata, ontology) { - new("MbioDataset", collections = veupathUtils::Collections(collections, data.table::fread(ontology)), metadata = sampleMetadataFromDataSources(list(metadata))) + new("MbioDataset", collections = mbioUtils::Collections(collections, data.table::fread(ontology)), metadata = sampleMetadataFromDataSources(list(metadata))) }) #' @rdname MbioDataset-methods #' @aliases MbioDataset,character,list,missing-method setMethod("MbioDataset", signature("character", "list", "missing"), function(collections, metadata, ontology) { - new("MbioDataset", collections = veupathUtils::Collections(collections), metadata = sampleMetadataFromDataSources(metadata)) + new("MbioDataset", collections = mbioUtils::Collections(collections), metadata = sampleMetadataFromDataSources(metadata)) }) #' @rdname MbioDataset-methods #' @aliases MbioDataset,character,list,data.frame-method setMethod("MbioDataset", signature("character", "list", "data.frame"), function(collections, metadata, ontology) { - new("MbioDataset", collections = veupathUtils::Collections(collections, ontology), metadata = sampleMetadataFromDataSources(metadata)) + new("MbioDataset", collections = mbioUtils::Collections(collections, ontology), metadata = sampleMetadataFromDataSources(metadata)) }) #' @rdname MbioDataset-methods #' @aliases MbioDataset,character,list,character-method setMethod("MbioDataset", signature("character", "list", "character"), function(collections, metadata, ontology) { - new("MbioDataset", collections = veupathUtils::Collections(collections, data.table::fread(ontology)), metadata = sampleMetadataFromDataSources(metadata)) + new("MbioDataset", collections = mbioUtils::Collections(collections, data.table::fread(ontology)), metadata = sampleMetadataFromDataSources(metadata)) }) #' @rdname MbioDataset-methods #' @aliases MbioDataset,character,missing,missing-method setMethod("MbioDataset", signature("character", "missing", "missing"), function(collections, metadata, ontology) { - new("MbioDataset", collections = veupathUtils::Collections(collections)) + new("MbioDataset", collections = mbioUtils::Collections(collections)) }) #' @rdname MbioDataset-methods #' @aliases MbioDataset,character,missing,data.frame-method setMethod("MbioDataset", signature("character", "missing", "data.frame"), function(collections, metadata, ontology) { - new("MbioDataset", collections = veupathUtils::Collections(collections, ontology), metadata = sampleMetadataBuilder(metadata)) + new("MbioDataset", collections = mbioUtils::Collections(collections, ontology), metadata = sampleMetadataBuilder(metadata)) }) #' @rdname MbioDataset-methods #' @aliases MbioDataset,character,missing,character-method setMethod("MbioDataset", signature("character", "missing", "character"), function(collections, metadata, ontology) { - new("MbioDataset", collections = veupathUtils::Collections(collections, data.table::fread(ontology)), metadata = sampleMetadataBuilder(metadata)) + new("MbioDataset", collections = mbioUtils::Collections(collections, data.table::fread(ontology)), metadata = sampleMetadataBuilder(metadata)) }) #' @rdname MbioDataset-methods #' @aliases MbioDataset,character,data.frame,missing-method setMethod("MbioDataset", signature("character", "data.frame", "missing"), function(collections, metadata, ontology) { - new("MbioDataset", collections = veupathUtils::Collections(collections), metadata = sampleMetadataBuilder(metadata)) + new("MbioDataset", collections = mbioUtils::Collections(collections), metadata = sampleMetadataBuilder(metadata)) }) #' @rdname MbioDataset-methods #' @aliases MbioDataset,character,data.frame,data.frame-method setMethod("MbioDataset", signature("character", "data.frame", "data.frame"), function(collections, metadata, ontology) { - new("MbioDataset", collections = veupathUtils::Collections(collections, ontology), metadata = sampleMetadataBuilder(metadata)) + new("MbioDataset", collections = mbioUtils::Collections(collections, ontology), metadata = sampleMetadataBuilder(metadata)) }) #' @rdname MbioDataset-methods #' @aliases MbioDataset,character,data.frame,character-method setMethod("MbioDataset", signature("character", "data.frame", "character"), function(collections, metadata, ontology) { - new("MbioDataset", collections = veupathUtils::Collections(collections, data.table::fread(ontology)), metadata = sampleMetadataBuilder(metadata)) + new("MbioDataset", collections = mbioUtils::Collections(collections, data.table::fread(ontology)), metadata = sampleMetadataBuilder(metadata)) }) #' @rdname MbioDataset-methods #' @aliases MbioDataset,character,SampleMetadata,missing-method setMethod("MbioDataset", signature("character", "SampleMetadata", "missing"), function(collections, metadata, ontology) { - new("MbioDataset", collections = veupathUtils::Collections(collections), metadata = metadata) + new("MbioDataset", collections = mbioUtils::Collections(collections), metadata = metadata) }) #' @rdname MbioDataset-methods #' @aliases MbioDataset,character,SampleMetadata,data.frame-method setMethod("MbioDataset", signature("character", "SampleMetadata", "data.frame"), function(collections, metadata, ontology) { - new("MbioDataset", collections = veupathUtils::Collections(collections, ontology), metadata = metadata) + new("MbioDataset", collections = mbioUtils::Collections(collections, ontology), metadata = metadata) }) #' @rdname MbioDataset-methods #' @aliases MbioDataset,character,SampleMetadata,character-method setMethod("MbioDataset", signature("character", "SampleMetadata", "character"), function(collections, metadata, ontology) { - new("MbioDataset", collections = veupathUtils::Collections(collections, data.table::fread(ontology)), metadata = metadata) + new("MbioDataset", collections = mbioUtils::Collections(collections, data.table::fread(ontology)), metadata = metadata) }) \ No newline at end of file diff --git a/R/importers-MbioDataset.R b/R/importers-MbioDataset.R index 326a026..35b90c1 100644 --- a/R/importers-MbioDataset.R +++ b/R/importers-MbioDataset.R @@ -6,7 +6,7 @@ buildCollectionFromTreeSE <- function( normalizationMethod = c("TSS", "none"), verbose = c(TRUE, FALSE) ) { - verbose <- veupathUtils::matchArg(verbose) + verbose <- mbioUtils::matchArg(verbose) assayDataName <- collectionName$assayDataName rowDataColumnName <- collectionName$rowDataColumnName @@ -66,7 +66,7 @@ buildCollectionFromTreeSE <- function( collectionName <- paste0(collectionName, " (", normalizationMethod, " normalized)") } - collection <- veupathUtils::Collection( + collection <- mbioUtils::Collection( data = dt, recordIdColumn = recordIdColumn, ancestorIdColumns = ancestorIdColumns, @@ -125,9 +125,9 @@ buildCollectionFromTreeSE <- function( #' @export importTreeSummarizedExperiment <- function(data, normalizationMethod = c("TSS", "none"), keepRawValues = c(TRUE, FALSE), verbose = c(TRUE, FALSE)) { - normalizationMethod <- veupathUtils::matchArg(normalizationMethod) - keepRawValues <- veupathUtils::matchArg(keepRawValues) - verbose <- veupathUtils::matchArg(verbose) + normalizationMethod <- mbioUtils::matchArg(normalizationMethod) + keepRawValues <- mbioUtils::matchArg(keepRawValues) + verbose <- mbioUtils::matchArg(verbose) if (!inherits(data, "SummarizedExperiment")) { stop("data must be or extend a SummarizedExperiment") @@ -182,7 +182,7 @@ importTreeSummarizedExperiment <- function(data, normalizationMethod = c("TSS", collectionsList <- c(rawCollectionsList, normalizedCollectionsList) } else { - collectionsList <- veupathUtils::Collections() + collectionsList <- mbioUtils::Collections() } diff --git a/R/method-differentialAbundance.R b/R/method-differentialAbundance.R index 16e9b8c..f2c342c 100644 --- a/R/method-differentialAbundance.R +++ b/R/method-differentialAbundance.R @@ -31,23 +31,23 @@ assignToBinaryGroups <- function(x, groupAPredicate, groupBPredicate = NULL) { return(x) } -#' @importFrom veupathUtils VariableSpec -#' @importFrom veupathUtils getIdColumns +#' @importFrom mbioUtils VariableSpec +#' @importFrom mbioUtils getIdColumns buildBinaryComparator <- function(covariate, groupAValue, groupBValue) { - binA <- veupathUtils::Bin(binLabel=groupAValue) - binB <- veupathUtils::Bin(binLabel=groupBValue) + binA <- mbioUtils::Bin(binLabel=groupAValue) + binB <- mbioUtils::Bin(binLabel=groupBValue) - groupABins <- veupathUtils::BinList(S4Vectors::SimpleList(c(binA))) - groupBBins <- veupathUtils::BinList(S4Vectors::SimpleList(c(binB))) + groupABins <- mbioUtils::BinList(S4Vectors::SimpleList(c(binA))) + groupBBins <- mbioUtils::BinList(S4Vectors::SimpleList(c(binB))) comparatorVariable <- microbiomeComputations::Comparator( - variable = veupathUtils::VariableMetadata( + variable = mbioUtils::VariableMetadata( variableSpec = VariableSpec( variableId = covariate, entityId = '' ), - dataShape = veupathUtils::DataShape(value="CATEGORICAL") + dataShape = mbioUtils::DataShape(value="CATEGORICAL") ), groupA = groupABins, groupB = groupBBins @@ -156,8 +156,8 @@ function(data, covariate, groupA, groupB, method = c("Maaslin2", "DESeq2"), verb #' @aliases differentialAbundance,CollectionWithMetadata,character,missingOrNULL,missingOrNULL-method setMethod("differentialAbundance", signature("CollectionWithMetadata", "character", "missingOrNULL", "missingOrNULL"), function(data, covariate, groupA, groupB, method = c("Maaslin2", "DESeq2"), verbose = c(TRUE, FALSE)) { - method <- veupathUtils::matchArg(method) - verbose <- veupathUtils::matchArg(verbose) + method <- mbioUtils::matchArg(method) + verbose <- mbioUtils::matchArg(verbose) if (data.table::uniqueN(data@sampleMetadata@data[[covariate]]) < 2) { stop("Argument 'covariate' must have at least two unique values") @@ -176,8 +176,8 @@ function(data, covariate, groupA, groupB, method = c("Maaslin2", "DESeq2"), verb #' @aliases differentialAbundance,CollectionWithMetadata,character,function,missingOrNULL-method setMethod("differentialAbundance", signature("CollectionWithMetadata", "character", "function", "missingOrNULL"), function(data, covariate, groupA, groupB, method = c("Maaslin2", "DESeq2"), verbose = c(TRUE, FALSE)) { - method <- veupathUtils::matchArg(method) - verbose <- veupathUtils::matchArg(verbose) + method <- mbioUtils::matchArg(method) + verbose <- mbioUtils::matchArg(verbose) if (data.table::uniqueN(data@sampleMetadata@data[[covariate]]) < 2) { stop("Argument 'covariate' must have at least two unique values") @@ -193,8 +193,8 @@ function(data, covariate, groupA, groupB, method = c("Maaslin2", "DESeq2"), verb #' @aliases differentialAbundance,CollectionWithMetadata,character,character,missingOrNULL-method setMethod("differentialAbundance", signature("CollectionWithMetadata", "character", "character", "missingOrNULL"), function(data, covariate, groupA, groupB, method = c("Maaslin2", "DESeq2"), verbose = c(TRUE, FALSE)) { - method <- veupathUtils::matchArg(method) - verbose <- veupathUtils::matchArg(verbose) + method <- mbioUtils::matchArg(method) + verbose <- mbioUtils::matchArg(verbose) covariateDataType <- class(data@sampleMetadata@data[[covariate]]) if (!covariateDataType %in% c("factor", "character")) { @@ -215,8 +215,8 @@ function(data, covariate, groupA, groupB, method = c("Maaslin2", "DESeq2"), verb #' @aliases differentialAbundance,CollectionWithMetadata,character,function,function-method setMethod("differentialAbundance", signature("CollectionWithMetadata", "character", "function", "function"), function(data, covariate, groupA, groupB, method = c("Maaslin2", "DESeq2"), verbose = c(TRUE, FALSE)) { - method <- veupathUtils::matchArg(method) - verbose <- veupathUtils::matchArg(verbose) + method <- mbioUtils::matchArg(method) + verbose <- mbioUtils::matchArg(verbose) if (data.table::uniqueN(data@sampleMetadata@data[[covariate]]) < 2) { stop("Argument 'covariate' must have at least two unique values") @@ -233,8 +233,8 @@ function(data, covariate, groupA, groupB, method = c("Maaslin2", "DESeq2"), verb #' @aliases differentialAbundance,CollectionWithMetadata,character,character,character-method setMethod("differentialAbundance", signature("CollectionWithMetadata", "character", "character", "character"), function(data, covariate, groupA, groupB, method = c("Maaslin2", "DESeq2"), verbose = c(TRUE, FALSE)) { - method <- veupathUtils::matchArg(method) - verbose <- veupathUtils::matchArg(verbose) + method <- mbioUtils::matchArg(method) + verbose <- mbioUtils::matchArg(verbose) covariateDataType <- class(data@sampleMetadata@data[[covariate]]) if (!covariateDataType %in% c("factor", "character")) { @@ -297,12 +297,12 @@ setGeneric("Maaslin2", function(data, verbose = c(TRUE,FALSE), ...) standardGene #' @rdname Maaslin2 #' @aliases Maaslin2,CollectionWithMetadata-method setMethod("Maaslin2", signature("CollectionWithMetadata"), function(data, verbose = c(TRUE,FALSE), ...) { - verbose <- veupathUtils::matchArg(verbose) + verbose <- mbioUtils::matchArg(verbose) recordIdColumn <- data@recordIdColumn ancestorIdColumns <- data@ancestorIdColumns allIdColumns <- c(recordIdColumn, ancestorIdColumns) - sampleMetadata <- veupathUtils::getSampleMetadata(data) + sampleMetadata <- mbioUtils::getSampleMetadata(data) abundances <- microbiomeComputations::getAbundances(data) # remove rows in sampleMetadata where covariate is NA or empty string @@ -353,12 +353,12 @@ setGeneric("DESeqDataSetFromCollection", function(data, verbose = c(TRUE,FALSE), #' @rdname DESeqDataSetFromCollection #' @aliases DESeqDataSetFromCollection,AbsoluteAbundanceData-method setMethod("DESeqDataSetFromCollection", signature("AbsoluteAbundanceData"), function(data, verbose = c(TRUE,FALSE), ...) { - verbose <- veupathUtils::matchArg(verbose) + verbose <- mbioUtils::matchArg(verbose) recordIdColumn <- data@recordIdColumn ancestorIdColumns <- data@ancestorIdColumns allIdColumns <- c(recordIdColumn, ancestorIdColumns) - sampleMetadata <- veupathUtils::getSampleMetadata(data) + sampleMetadata <- mbioUtils::getSampleMetadata(data) abundances <- microbiomeComputations::getAbundances(data, verbose = verbose) # First, remove id columns and any columns that are all 0s. @@ -375,7 +375,7 @@ setMethod("DESeqDataSetFromCollection", signature("AbsoluteAbundanceData"), func # expects the order to match, and will not perform this check. if (!identical(rownames(sampleMetadata), colnames(counts))){ # Reorder sampleMetadata to match counts - veupathUtils::logWithTime("Sample order differs between data and metadata. Reordering data based on the metadata sample order.", verbose) + mbioUtils::logWithTime("Sample order differs between data and metadata. Reordering data based on the metadata sample order.", verbose) data.table::setcolorder(counts, rownames(sampleMetadata)) } diff --git a/R/methods-ComputeResult.R b/R/methods-ComputeResult.R index 4614c8c..a6e0fd5 100644 --- a/R/methods-ComputeResult.R +++ b/R/methods-ComputeResult.R @@ -17,7 +17,7 @@ #' @param format The format of the compute result. Currently only "data.table" and "igraph" are supported. #' @param ... additional arguments passed to getComputeResult method of the subclasses of ComputeResult #' @return The compute result in the specified format -#' @importFrom veupathUtils matchArg ComputeResult +#' @importFrom mbioUtils matchArg ComputeResult #' @export #' @rdname getComputeResult setGeneric("getComputeResult", function(object, format = c("data.table"), ...) standardGeneric("getComputeResult")) @@ -26,7 +26,7 @@ setGeneric("getComputeResult", function(object, format = c("data.table"), ...) s #' @rdname getComputeResult #' @aliases getComputeResult,ComputeResult-method setMethod("getComputeResult", "ComputeResult", function(object, format = c("data.table", "igraph"), ...) { - format <- veupathUtils::matchArg(format) + format <- mbioUtils::matchArg(format) if (!!length(object@statistics)) { return(getComputeResult(object@statistics, format, ...)) @@ -41,7 +41,7 @@ setMethod("getComputeResult", "ComputeResult", function(object, format = c("data return(dt) }) -#' @importFrom veupathUtils CorrelationResult +#' @importFrom mbioUtils CorrelationResult #' @rdname getComputeResult #' @param correlationCoefThreshold threshold to filter edges by correlation coefficient. #' Edges with correlation coefficients below this threshold will be removed. Default is .5 @@ -49,7 +49,7 @@ setMethod("getComputeResult", "ComputeResult", function(object, format = c("data #' @aliases getComputeResult,CorrelationResult-method #' @importFrom igraph graph_from_data_frame setMethod("getComputeResult", "CorrelationResult", function(object, format = c("data.table", "igraph"), correlationCoefThreshold = .5, pValueThreshold = .05) { - format <- veupathUtils::matchArg(format) + format <- mbioUtils::matchArg(format) result <- data.table::setDT(object@statistics) @@ -66,17 +66,17 @@ setMethod("getComputeResult", "CorrelationResult", function(object, format = c(" #' @rdname getComputeResult #' @aliases getComputeResult,DifferentialAbundanceResult-method setMethod("getComputeResult", "DifferentialAbundanceResult", function(object, format = c("data.table")) { - format <- veupathUtils::matchArg(format) + format <- mbioUtils::matchArg(format) return(data.table::setDT(object@statistics)) }) -#' @importFrom veupathUtils getSampleMetadata -#' @importFrom veupathUtils getSampleMetadataIdColumns +#' @importFrom mbioUtils getSampleMetadata +#' @importFrom mbioUtils getSampleMetadataIdColumns mergeComputeResultAndMetadata <- function(computeResult, dataset, metadataVariables) { dt <- getComputeResult(computeResult, "data.table") - metadata <- veupathUtils::getSampleMetadata(dataset, includeIds = TRUE, metadataVariables = metadataVariables) + metadata <- mbioUtils::getSampleMetadata(dataset, includeIds = TRUE, metadataVariables = metadataVariables) - metadataIdColumns <- veupathUtils::getSampleMetadataIdColumns(dataset) + metadataIdColumns <- mbioUtils::getSampleMetadataIdColumns(dataset) dt <- merge(dt, metadata, by = metadataIdColumns, all.x = TRUE) return(dt) @@ -117,7 +117,7 @@ function(object, dataset, format = c("data.table"), metadataVariables = NULL) #' @aliases getComputeResultWithMetadata,ComputeResult,MbioDataset-method setMethod("getComputeResultWithMetadata", signature = c("ComputeResult", "MbioDataset"), function(object, dataset = NULL, format = c("data.table"), metadataVariables = NULL) { - format <- veupathUtils::matchArg(format) + format <- mbioUtils::matchArg(format) dt <- mergeComputeResultAndMetadata(object, dataset, metadataVariables) return(dt) @@ -127,7 +127,7 @@ function(object, dataset = NULL, format = c("data.table"), metadataVariables = N #' @aliases getComputeResultWithMetadata,ComputeResult,Collection-method setMethod("getComputeResultWithMetadata", signature = c("ComputeResult", "Collection"), function(object, dataset = NULL, format = c("data.table"), metadataVariables = NULL) { - format <- veupathUtils::matchArg(format) + format <- mbioUtils::matchArg(format) dt <- mergeComputeResultAndMetadata(object, dataset, metadataVariables) return(dt) @@ -137,7 +137,7 @@ function(object, dataset = NULL, format = c("data.table"), metadataVariables = N #' @aliases getComputeResultWithMetadata,ComputeResult,AbundanceData-method setMethod("getComputeResultWithMetadata", signature = c("ComputeResult", "AbundanceData"), function(object, dataset = NULL, format = c("data.table"), metadataVariables = NULL) { - format <- veupathUtils::matchArg(format) + format <- mbioUtils::matchArg(format) dt <- mergeComputeResultAndMetadata(object, dataset, metadataVariables) return(dt) @@ -196,7 +196,7 @@ setMethod("correlationNetwork", "data.frame", function( pValueThreshold = .05, bipartiteNetwork = c(FALSE, TRUE) ) { - bipartiteNetwork <- veupathUtils::matchArg(bipartiteNetwork) + bipartiteNetwork <- mbioUtils::matchArg(bipartiteNetwork) warning("data.frame input assumes the columns are in the following order: source, target, correlationCoef, pValue.") names(object) <- c("source", "target", "value", "pValue") diff --git a/R/methods-MbioDataset.R b/R/methods-MbioDataset.R index 1ba26fd..8ac6525 100644 --- a/R/methods-MbioDataset.R +++ b/R/methods-MbioDataset.R @@ -1,4 +1,4 @@ -collectionNamesGeneric <- getGeneric("getCollectionNames", "veupathUtils") +collectionNamesGeneric <- getGeneric("getCollectionNames", "mbioUtils") #' Get Names of Collections #' #' Get the names of the collections in a MbioDataset object @@ -8,10 +8,10 @@ collectionNamesGeneric <- getGeneric("getCollectionNames", "veupathUtils") #' @param object An MbioDataset #' @return A character vector of collection names #' @export -#' @importFrom veupathUtils getCollectionNames +#' @importFrom mbioUtils getCollectionNames setMethod(collectionNamesGeneric, "MbioDataset", function(object) return(unname(getCollectionNames(object@collections)))) -metadataVarNamesGeneric <- getGeneric("getMetadataVariableNames", "veupathUtils") +metadataVarNamesGeneric <- getGeneric("getMetadataVariableNames", "mbioUtils") #' Get Variable Names of Metadata #' #' Get the names of the metadata variables in an MbioDataset. @@ -21,10 +21,10 @@ metadataVarNamesGeneric <- getGeneric("getMetadataVariableNames", "veupathUtils" #' @param object An MbioDataset #' @return a character vector of metadata variable names #' @export -#' @importFrom veupathUtils getMetadataVariableNames +#' @importFrom mbioUtils getMetadataVariableNames setMethod(metadataVarNamesGeneric, "MbioDataset", function(object) return(names(object@metadata@data))) -metadataVarSummaryGeneric <- getGeneric("getMetadataVariableSummary", "veupathUtils") +metadataVarSummaryGeneric <- getGeneric("getMetadataVariableSummary", "mbioUtils") #' Get Summary of Metadata Variables #' #' Get a summary of the requested metadata variable in an MbioDataset. @@ -37,7 +37,7 @@ metadataVarSummaryGeneric <- getGeneric("getMetadataVariableSummary", "veupathUt #' @param variable A character vector representing the name of the metadata variable to summarize #' @return a table summarizing the values of the requested metadata variable #' @export -#' @importFrom veupathUtils getMetadataVariableSummary +#' @importFrom mbioUtils getMetadataVariableSummary setMethod(metadataVarSummaryGeneric, "MbioDataset", function(object, variable) { if (!variable %in% getMetadataVariableNames(object)) { stop("Variable ", variable, " not found in sample metadata. Available variables: ", paste(getMetadataVariableNames(object), collapse = ", ")) @@ -54,7 +54,7 @@ setMethod(metadataVarSummaryGeneric, "MbioDataset", function(object, variable) { } }) -sampleMetadataGeneric <- getGeneric("getSampleMetadata", "veupathUtils") +sampleMetadataGeneric <- getGeneric("getSampleMetadata", "mbioUtils") #' Get data.table of sample metadata from MbioDataset #' #' Returns a data.table of sample metadata @@ -69,13 +69,13 @@ sampleMetadataGeneric <- getGeneric("getSampleMetadata", "veupathUtils") #' @return data.table of sample metadata #' @export setMethod(sampleMetadataGeneric, "MbioDataset", function(object, asCopy = c(TRUE, FALSE), includeIds = c(TRUE, FALSE), metadataVariables = NULL) { - asCopy <- veupathUtils::matchArg(asCopy) - includeIds <- veupathUtils::matchArg(includeIds) + asCopy <- mbioUtils::matchArg(asCopy) + includeIds <- mbioUtils::matchArg(includeIds) if (!length(object@metadata@data)) return(NULL) dt <- object@metadata@data - allIdColumns <- veupathUtils::getSampleMetadataIdColumns(object) + allIdColumns <- mbioUtils::getSampleMetadataIdColumns(object) # Check that incoming dt meets requirements if (!inherits(dt, 'data.table')) { @@ -97,13 +97,13 @@ setMethod(sampleMetadataGeneric, "MbioDataset", function(object, asCopy = c(TRUE return(dt) }) -metadataIdColsGeneric <- getGeneric("getSampleMetadataIdColumns", "veupathUtils") +metadataIdColsGeneric <- getGeneric("getSampleMetadataIdColumns", "mbioUtils") #' Get Sample Metadata Id Column Names #' #' Get the names of the record and ancestor id columns in the sample metadata of an MbioDataset object. #' @param object MbioDataset #' @return a character vector of id column names -setMethod(metadataIdColsGeneric, "MbioDataset", function(object) veupathUtils::getIdColumns(object@metadata)) +setMethod(metadataIdColsGeneric, "MbioDataset", function(object) mbioUtils::getIdColumns(object@metadata)) #' Update Microbiome Dataset Collection Name @@ -175,8 +175,8 @@ setGeneric("getCollection", function(object, collectionName, format = c("Abundan #' @rdname getCollection #' @aliases getCollection,MbioDataset,character-method setMethod("getCollection", "MbioDataset", function(object, collectionName = character(0), format = c("AbundanceData", "phyloseq", "Collection"), continuousMetadataOnly = c(FALSE, TRUE)) { - format <- veupathUtils::matchArg(format) - continuousMetadataOnly <- veupathUtils::matchArg(continuousMetadataOnly) + format <- mbioUtils::matchArg(format) + continuousMetadataOnly <- mbioUtils::matchArg(continuousMetadataOnly) if (length(collectionName) == 0) { stop("Must specify a collection name") @@ -240,7 +240,7 @@ setMethod("getCollection", "MbioDataset", function(object, collectionName = char collectionDataDT <- collectionDT[, -collectionIdColumns, with = FALSE] if (all(collectionDataDT == round(collectionDataDT), na.rm = TRUE)) { - veupathUtils::logWithTime("Integer values detected. Converting collection to AbsoluteAbundanceData", verbose = TRUE) + mbioUtils::logWithTime("Integer values detected. Converting collection to AbsoluteAbundanceData", verbose = TRUE) abundanceData <- AbsoluteAbundanceData( name = collection@name, data = collectionDT, @@ -292,7 +292,7 @@ setMethod("getCollection", "MbioDataset", function(object, collectionName = char return(abundanceData) }) -collectionVarNamesGeneric <- getGeneric("getCollectionVariableNames", "veupathUtils") +collectionVarNamesGeneric <- getGeneric("getCollectionVariableNames", "mbioUtils") #' Get Microbiome Dataset Collection Variable Names #' #' Get the variable names in a collection in the Microbiome Dataset. @@ -306,9 +306,9 @@ collectionVarNamesGeneric <- getGeneric("getCollectionVariableNames", "veupathUt #' @param collectionName The name of the collection to return the variable names for #' @return a character vector of the variable names in the requested collection #' @export -#' @importFrom veupathUtils getCollectionVariableNames +#' @importFrom mbioUtils getCollectionVariableNames setMethod(collectionVarNamesGeneric, "MbioDataset", function(object, collectionName) { - return(veupathUtils::getCollectionVariableNames(getCollection(object, collectionName))) + return(mbioUtils::getCollectionVariableNames(getCollection(object, collectionName))) }) #' Get Microbiome Dataset Variables @@ -375,11 +375,11 @@ setMethod("getVariables", "MbioDataset", function(object, variables) { if (any(variableNames %in% getCollectionVariableNames(object, collectionName))) { collection <- getCollection(object, collectionName) presentVars <- variableNames[variableNames %in% getCollectionVariableNames(collection)] - if (veupathUtils::isOneToManyWithAncestor(collection)) { + if (mbioUtils::isOneToManyWithAncestor(collection)) { warning("Unable to return the following variables: ", presentVars) return(data.table::data.table()) } - dt <- veupathUtils::getCollectionData(collection, presentVars) + dt <- mbioUtils::getCollectionData(collection, presentVars) if (collectionIndex %in% collectionsWithDupsIndexes) { ## rename variables to prepend the collection name names(dt)[names(dt) %in% presentVars] <- paste(collectionName, presentVars) diff --git a/R/reexports-microbiomeComputations.R b/R/reexports-microbiomeComputations.R index 1b71178..d8beaf2 100644 --- a/R/reexports-microbiomeComputations.R +++ b/R/reexports-microbiomeComputations.R @@ -97,15 +97,15 @@ microbiomeComputations::betaDiv #' @param verbose boolean indicating if timed logging is desired #' @param ... additional parameters #' @return data.frame with correlation coefficients or a ComputeResult object -#' @importFrom veupathUtils correlation +#' @importFrom mbioUtils correlation #' @export #' @rdname correlation-methods -veupathUtils::correlation +mbioUtils::correlation #' Self Correlation #' #' This function returns correlation coefficients for variables in one AbundanceData object against itself. It generally serves as a -#' convenience wrapper around veupathUtils::correlation, with the exception that it additionally supports sparcc. +#' convenience wrapper around mbioUtils::correlation, with the exception that it additionally supports sparcc. #' #' @examples #' correlationDT <- selfCorrelation( @@ -134,8 +134,8 @@ veupathUtils::correlation #' @param verbose boolean indicating if timed logging is desired #' @param ... additional parameters #' @return ComputeResult object -#' @importFrom veupathUtils selfCorrelation +#' @importFrom mbioUtils selfCorrelation #' @importFrom microbiomeComputations selfCorrelation #' @export #' @rdname selfCorrelation-methods -veupathUtils::selfCorrelation +mbioUtils::selfCorrelation From 2514799db7c892a9dfbfc6666621110a44df054d Mon Sep 17 00:00:00 2001 From: Danielle Callan Date: Fri, 21 Nov 2025 12:01:14 -0500 Subject: [PATCH 4/7] update tests for dep change --- tests/testthat/test-GetComputeResult.R | 14 +++++++------- tests/testthat/test-differentialAbundance.R | 2 +- tests/testthat/test-importers-MbioDataset.R | 2 ++ 3 files changed, 10 insertions(+), 8 deletions(-) diff --git a/tests/testthat/test-GetComputeResult.R b/tests/testthat/test-GetComputeResult.R index f670bbb..638ccdd 100644 --- a/tests/testthat/test-GetComputeResult.R +++ b/tests/testthat/test-GetComputeResult.R @@ -13,23 +13,23 @@ test_that("we can get compute results in different formats", { expect_equal(all(grepl('[',names(genus@sampleMetadata@data),fixed=T)), FALSE) # and that that means diff abund works now comparatorVariable <- microbiomeComputations::Comparator( - variable = veupathUtils::VariableMetadata( - variableSpec = veupathUtils::VariableSpec( + variable = mbioUtils::VariableMetadata( + variableSpec = mbioUtils::VariableSpec( variableId = 'delivery_mode', entityId = '' ), - dataShape = veupathUtils::DataShape(value="BINARY") + dataShape = mbioUtils::DataShape(value="BINARY") ), - groupA = veupathUtils::BinList( + groupA = mbioUtils::BinList( S4Vectors::SimpleList( - c(veupathUtils::Bin( + c(mbioUtils::Bin( binLabel="Vaginal" )) ) ), - groupB = veupathUtils::BinList( + groupB = mbioUtils::BinList( S4Vectors::SimpleList( - c(veupathUtils::Bin( + c(mbioUtils::Bin( binLabel="Cesarean" )) ) diff --git a/tests/testthat/test-differentialAbundance.R b/tests/testthat/test-differentialAbundance.R index d0a65a2..bbf9f52 100644 --- a/tests/testthat/test-differentialAbundance.R +++ b/tests/testthat/test-differentialAbundance.R @@ -9,7 +9,7 @@ mbioDataset <- MbioDataset(list(dataFile1, dataFile2), list(metadataFile2, metad genus <- getCollection(mbioDataset, "16S (V4) Genus (Relative taxonomic abundance analysis)") -genusIdCols <- veupathUtils::getIdColumns(genus) +genusIdCols <- mbioUtils::getIdColumns(genus) counts <- round(microbiomeComputations::getAbundances(genus, includeIds=FALSE)*1000) counts <- cbind(genus@data[, genusIdCols, with=FALSE], counts) genusCounts <- AbsoluteAbundanceData( diff --git a/tests/testthat/test-importers-MbioDataset.R b/tests/testthat/test-importers-MbioDataset.R index 93ceee8..2c3a524 100644 --- a/tests/testthat/test-importers-MbioDataset.R +++ b/tests/testthat/test-importers-MbioDataset.R @@ -57,6 +57,8 @@ test_that("buildCollectionFromTreeSE works", { }) test_that("we can get an MbioDataset from a TreeSummarizedExperiment", { + skip_if_not_installed("mia") + data(GlobalPatterns, package="mia") tse <- GlobalPatterns From 0d847518666795c2f57c068d6f686cdb78243d32 Mon Sep 17 00:00:00 2001 From: Danielle Callan Date: Fri, 21 Nov 2025 12:01:27 -0500 Subject: [PATCH 5/7] update docs and version --- DESCRIPTION | 8 +++---- NAMESPACE | 38 +++++++++++++++++----------------- man/selfCorrelation-methods.Rd | 2 +- 3 files changed, 24 insertions(+), 24 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 6b44168..f77437c 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -12,15 +12,15 @@ Imports: data.table, DESeq2, igraph, - veupathUtils (>= 2.7.0), + mbioUtils (>= 0.1.0), Maaslin2, methods, - microbiomeComputations (>= 5.1.6), + microbiomeComputations (>= 5.1.7), purrr, SummarizedExperiment, TreeSummarizedExperiment Remotes: - VEuPathDB/veupathUtils, + microbiomeDB/mbioUtils, microbiomeDB/corGraph, microbiomeDB/microbiomeComputations, microbiomeDB/microbiomeData, @@ -31,7 +31,7 @@ Description: This package is intended to be used to explore the curated datasets License: Apache License (>= 2) Encoding: UTF-8 Roxygen: list(markdown = TRUE) -RoxygenNote: 7.3.1 +RoxygenNote: 7.3.3 Suggests: testthat (>= 3.0.0), S4Vectors, diff --git a/NAMESPACE b/NAMESPACE index b85fde1..1c0e040 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -38,6 +38,25 @@ importFrom(corGraph,bipartiteNetwork) importFrom(corGraph,unipartiteNetwork) importFrom(data.table,data.table) importFrom(igraph,graph_from_data_frame) +importFrom(mbioUtils,Collection) +importFrom(mbioUtils,Collections) +importFrom(mbioUtils,ComputeResult) +importFrom(mbioUtils,CorrelationResult) +importFrom(mbioUtils,SampleMetadata) +importFrom(mbioUtils,VariableSpec) +importFrom(mbioUtils,correlation) +importFrom(mbioUtils,findAncestorIdColumns) +importFrom(mbioUtils,findRecordIdColumn) +importFrom(mbioUtils,getCollectionNames) +importFrom(mbioUtils,getCollectionVariableNames) +importFrom(mbioUtils,getDataFromSource) +importFrom(mbioUtils,getIdColumns) +importFrom(mbioUtils,getMetadataVariableNames) +importFrom(mbioUtils,getMetadataVariableSummary) +importFrom(mbioUtils,getSampleMetadata) +importFrom(mbioUtils,getSampleMetadataIdColumns) +importFrom(mbioUtils,matchArg) +importFrom(mbioUtils,selfCorrelation) importFrom(microbiomeComputations,AbsoluteAbundanceData) importFrom(microbiomeComputations,AbundanceData) importFrom(microbiomeComputations,Comparator) @@ -48,22 +67,3 @@ importFrom(microbiomeComputations,internalDiffAbund) importFrom(microbiomeComputations,rankedAbundance) importFrom(microbiomeComputations,selfCorrelation) importFrom(purrr,reduce) -importFrom(veupathUtils,Collection) -importFrom(veupathUtils,Collections) -importFrom(veupathUtils,ComputeResult) -importFrom(veupathUtils,CorrelationResult) -importFrom(veupathUtils,SampleMetadata) -importFrom(veupathUtils,VariableSpec) -importFrom(veupathUtils,correlation) -importFrom(veupathUtils,findAncestorIdColumns) -importFrom(veupathUtils,findRecordIdColumn) -importFrom(veupathUtils,getCollectionNames) -importFrom(veupathUtils,getCollectionVariableNames) -importFrom(veupathUtils,getDataFromSource) -importFrom(veupathUtils,getIdColumns) -importFrom(veupathUtils,getMetadataVariableNames) -importFrom(veupathUtils,getMetadataVariableSummary) -importFrom(veupathUtils,getSampleMetadata) -importFrom(veupathUtils,getSampleMetadataIdColumns) -importFrom(veupathUtils,matchArg) -importFrom(veupathUtils,selfCorrelation) diff --git a/man/selfCorrelation-methods.Rd b/man/selfCorrelation-methods.Rd index dcbe45e..80e0d5e 100644 --- a/man/selfCorrelation-methods.Rd +++ b/man/selfCorrelation-methods.Rd @@ -28,7 +28,7 @@ ComputeResult object } \description{ This function returns correlation coefficients for variables in one AbundanceData object against itself. It generally serves as a -convenience wrapper around veupathUtils::correlation, with the exception that it additionally supports sparcc. +convenience wrapper around mbioUtils::correlation, with the exception that it additionally supports sparcc. } \examples{ correlationDT <- selfCorrelation( From d6dbb4e6a62a5321cedf629ef8f68815b7e4cbc1 Mon Sep 17 00:00:00 2001 From: Danielle Callan Date: Fri, 21 Nov 2025 12:03:31 -0500 Subject: [PATCH 6/7] accidentally updated version twice lol --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index f77437c..b29d8ec 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: MicrobiomeDB Title: Curated Data and Analysis Tools from MicrobiomeDB.org -Version: 1.1.3 +Version: 1.1.2 Authors@R: c(person(given = "Danielle", family = "Callan", From 38d2df53fc9f3f46a58d08670cec926415b70e10 Mon Sep 17 00:00:00 2001 From: Danielle Callan Date: Fri, 21 Nov 2025 12:07:44 -0500 Subject: [PATCH 7/7] clarify deps --- DESCRIPTION | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index b29d8ec..181a366 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -23,8 +23,7 @@ Remotes: microbiomeDB/mbioUtils, microbiomeDB/corGraph, microbiomeDB/microbiomeComputations, - microbiomeDB/microbiomeData, - bioc::Maaslin2 + microbiomeDB/microbiomeData URL: https://github.com/microbiomeDB/MicrobiomeDB, https://microbiomedb.github.io/MicrobiomeDB/ BugReports: https://github.com/microbiomeDB/MicrobiomeDB/issues Description: This package is intended to be used to explore the curated datasets from MicrobiomeDB.org, as well as your own datasets. It comes pre-packaged with the same functions used to power the analysis tools from the website. It also contains functions to facilitate easily transforming data between our custom objects, phyloseq objects, and .biom files that you can upload to the website.