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Issue #174: TreeSE support non-taxonomic ranks #201

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merged 5 commits into from
Sep 16, 2023
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Issue #174: TreeSE support non-taxonomic ranks #201

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Issue 174: TreeSE support non-taxonomic ranks
Daenarys8 Aug 24, 2023
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Daenarys8 Aug 25, 2023
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Daenarys8 Aug 25, 2023
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Daenarys8 Aug 28, 2023
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Daenarys8 Sep 14, 2023
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10 changes: 5 additions & 5 deletions R/ancombc2.R
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Original file line number Diff line number Diff line change
Expand Up @@ -81,13 +81,13 @@
#' (only applicable if data object is a \code{(Tree)SummarizedExperiment}).
#' Default is "counts".
#' See \code{?SummarizedExperiment::assay} for more details.
#' @param tax_level character. The taxonomic level of interest. The input data
#' can be analyzed at any taxonomic level without prior agglomeration.
#' Note that \code{tax_level} must be a value from \code{taxonomyRanks}, which
#' includes "Kingdom", "Phylum" "Class", "Order", "Family" "Genus" or "Species".
#' @param tax_level character. The taxonomic or non taxonomic(rowData) level of interest. The input data
#' can be analyzed at any taxonomic or rowData level without prior agglomeration.
#' Note that \code{tax_level} must be a value from \code{taxonomyRanks} or \code{rowData}, which
#' includes "Kingdom", "Phylum" "Class", "Order", "Family" "Genus" "Species" etc.
#' See \code{?mia::taxonomyRanks} for more details.
#' Default is NULL, i.e., do not perform agglomeration, and the
#' ANCOM-BC2 anlysis will be performed at the lowest taxonomic level of the
#' ANCOM-BC2 analysis will be performed at the lowest taxonomic level of the
#' input \code{data}.
#' @param fix_formula the character string expresses how the microbial absolute
#' abundances for each taxon depend on the fixed effects in metadata. When
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20 changes: 2 additions & 18 deletions R/ancombc_prep.R
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Expand Up @@ -30,18 +30,10 @@ tse_construct = function(data, assay_name, tax_level, phyloseq) {

# Check if agglomeration should be performed
if (is.null(tax_level)) {
tax_levels = mia::taxonomyRanks(tse)
txt = sprintf(paste0("`tax_level` is not specified \n",
"No agglomeration will be performed",
"\n",
"Otherwise, please specify `tax_level` ",
"by one of the following: \n",
paste(tax_levels, collapse = ", ")))
message(txt)
tax_level = "ASV"
tse_alt = tse
} else {
tse_alt = mia::agglomerateByRank(tse, tax_level)
tse_alt = mia:::.merge_features(tse, tax_level)
}
SingleCellExperiment::altExp(tse, tax_level) = tse_alt
} else if (!is.null(phyloseq)) {
Expand All @@ -57,18 +49,10 @@ tse_construct = function(data, assay_name, tax_level, phyloseq) {
}

if (is.null(tax_level)) {
tax_levels = mia::taxonomyRanks(tse)
txt = sprintf(paste0("`tax_level` is not speficified \n",
"No agglomeration will be performed",
"\n",
"Otherwise, please speficy `tax_level` ",
"by one of the following: \n",
paste(tax_levels, collapse = ", ")))
message(txt)
tax_level = "ASV"
tse_alt = tse
} else {
tse_alt = mia::agglomerateByRank(tse, tax_level)
tse_alt = mia:::.merge_features(tse, tax_level)
}
SingleCellExperiment::altExp(tse, tax_level) = tse_alt
} else {
Expand Down