Merge pull request #16 from biobakery/devel

Changed assay_type to assay.type
biobakery · Jan 31, 2025 · b9b8e77 · b9b8e77
2 parents b90fb46 + 05599a9
commit b9b8e77
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Showing 6 changed files with 10 additions and 10 deletions.
diff --git a/R/maaslin3.R b/R/maaslin3.R
@@ -2660,7 +2660,7 @@ maaslin3 <- function(input_data,
                     save_plots_rds = FALSE,
                     verbosity = 'FINEST',
                     summary_plot_balanced = FALSE,
-                    assay_type = 1) {
+                    assay.type = 1) {
     match.arg(verbosity, c("FINEST", "FINER", "FINE", "DEBUG", "INFO",
                             "WARN", "ERROR"))
     logging::logReset()
@@ -2680,7 +2680,7 @@ maaslin3 <- function(input_data,
 
     if (inherits(input_data, "SummarizedExperiment")) {
         summarized_experiment_out <-
-            maaslin_read_summarized_experiment_data(input_data, assay_type)
+            maaslin_read_summarized_experiment_data(input_data, assay.type)
 
         input_data <- summarized_experiment_out[['data']]
         input_metadata <- summarized_experiment_out[['metadata']]

diff --git a/R/utility_scripts.R b/R/utility_scripts.R
@@ -825,12 +825,12 @@ preprocess_dna_mtx <- function(dna_table, rna_table) {
 # Read from SummarizedExperiment #
 ##################################
 
-maaslin_read_summarized_experiment_data <- function(summarized_experiment, assay_type = 1) {
+maaslin_read_summarized_experiment_data <- function(summarized_experiment, assay.type = 1) {
     if (!inherits(summarized_experiment, "SummarizedExperiment")) {
         stop("Input must be a SummarizedExperiment object")
     }
 
-    data <- as.data.frame(t(SummarizedExperiment::assay(summarized_experiment, assay_type)))
+    data <- as.data.frame(t(SummarizedExperiment::assay(summarized_experiment, assay.type)))
     metadata <- as.data.frame(
         SummarizedExperiment::colData(summarized_experiment))
     return(list(

diff --git a/README.md b/README.md
@@ -661,7 +661,7 @@ save them to an RData file.
 * `verbosity` (default `'FINEST'`): The level of verbosity for the 
 `logging` package.
 * `save_plots_rds` (default `FALSE`): Whether to save the plots as RDS files.
-* `assay_type` (default `1`): A string or index to select the assay when using
+* `assay.type` (default `1`): A string or index to select the assay when using
 a `SummarizedExperiment` object.
 
 ## Troubleshooting ##

diff --git a/man/maaslin3.Rd b/man/maaslin3.Rd
@@ -60,7 +60,7 @@ maaslin3(input_data,
     save_plots_rds = FALSE,
     verbosity = 'FINEST',
     summary_plot_balanced = FALSE,
-    assay_type = 1)
+    assay.type = 1)
 }
 \arguments{
     \item{input_data}{A data frame of feature abundances or read counts, a
@@ -223,7 +223,7 @@ maaslin3(input_data,
     \code{coef_plot_vars} where N is equal to: 
     \code{ceiling(summary_plot_first_n/length(coef_plot_vars))}. Will error
     if \code{coef_plot_vars} = \code{NULL}}
-    \item{assay_type}{A string or index to select the assay when using
+    \item{assay.type}{A string or index to select the assay when using
     a \code{SummarizedExperiment} object}
 }
 \value{

diff --git a/tests/testthat/test_Maaslin3.R b/tests/testthat/test_Maaslin3.R
@@ -82,7 +82,7 @@ fit_out <- maaslin3(input_data = tse,
                     median_comparison_prevalence = FALSE, 
                     cores=1, 
                     verbosity = 'WARN',
-                    assay_type = 'another_taxa_table')
+                    assay.type = 'another_taxa_table')
 
 fit_out <- maaslin3(input_data = tse, 
                     input_metadata = metadata, 
@@ -99,6 +99,6 @@ fit_out <- maaslin3(input_data = tse,
                     median_comparison_prevalence = FALSE, 
                     cores=1, 
                     verbosity = 'WARN',
-                    assay_type = 2)
+                    assay.type = 2)
 
 unlink(output_tmp, recursive = T)
diff --git a/vignettes/maaslin3_manual.Rmd b/vignettes/maaslin3_manual.Rmd
@@ -899,7 +899,7 @@ save them to an RData file.
 * `verbosity` (default `'FINEST'`): The level of verbosity for the 
 `logging` package.
 * `save_plots_rds` (default `FALSE`): Whether to save the plots as RDS files.
-* `assay_type` (default `1`): A string or index to select the assay when using
+* `assay.type` (default `1`): A string or index to select the assay when using
 a `SummarizedExperiment` object.
 
 ## Tool comparison ##