From d73d19eba9c612a59faf32fac3286327da0bcff4 Mon Sep 17 00:00:00 2001
From: Louise Huuki <lahuuki@gmail.com>
Date: Fri, 17 May 2024 15:44:26 -0400
Subject: [PATCH] Update function name add_qc_metrics in docs

---
 NAMESPACE                                |  2 +-
 R/add_qc_metrics.R                       |  4 ++--
 man/{metrics_qc.Rd => add_qc_metrics.Rd} | 10 +++++-----
 3 files changed, 8 insertions(+), 8 deletions(-)
 rename man/{metrics_qc.Rd => add_qc_metrics.Rd} (91%)

diff --git a/NAMESPACE b/NAMESPACE
index 4a9ab05e..4eba582c 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -3,6 +3,7 @@
 export(add10xVisiumAnalysis)
 export(add_images)
 export(add_key)
+export(add_qc_metrics)
 export(annotate_registered_clusters)
 export(check_modeling_results)
 export(check_sce)
@@ -25,7 +26,6 @@ export(layer_matrix_plot)
 export(layer_stat_cor)
 export(layer_stat_cor_plot)
 export(locate_images)
-export(metrics_qc)
 export(read10xVisiumAnalysis)
 export(read10xVisiumWrapper)
 export(registration_block_cor)
diff --git a/R/add_qc_metrics.R b/R/add_qc_metrics.R
index df7cf2f0..01067f87 100644
--- a/R/add_qc_metrics.R
+++ b/R/add_qc_metrics.R
@@ -26,7 +26,7 @@
 #'     spe_qc$in_tissue[spe_qc$array_col < 10] <- FALSE
 #'
 #'     ## adds QC metrics to colData of the spe
-#'     spe_qc <- add_qc_metrics()(spe_qc)
+#'     spe_qc <- add_qc_metrics(spe_qc)
 #'     colData(spe_qc)
 #'
 #'     ## visualize edge spots
@@ -43,7 +43,7 @@
 #'     vis_clus(spe_qc, sampleid = "151507", clustervar = "scran_low_lib_size_edge")
 #' }
 #' 
-add_qc_metrics() <- function(spe) {
+add_qc_metrics <- function(spe) {
     stopifnot("in_tissue" %in% colnames(colData(spe)))
     stopifnot("sum_umi" %in% colnames(colData(spe)))
     stopifnot("sum_gene" %in% colnames(colData(spe)))
diff --git a/man/metrics_qc.Rd b/man/add_qc_metrics.Rd
similarity index 91%
rename from man/metrics_qc.Rd
rename to man/add_qc_metrics.Rd
index db964436..b1d5dc5d 100644
--- a/man/metrics_qc.Rd
+++ b/man/add_qc_metrics.Rd
@@ -1,10 +1,10 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/metrics_qc.R
-\name{metrics_qc}
-\alias{metrics_qc}
+% Please edit documentation in R/add_qc_metrics.R
+\name{add_qc_metrics}
+\alias{add_qc_metrics}
 \title{Quality Control for Spatial Data}
 \usage{
-metrics_qc(spe)
+add_qc_metrics(spe)
 }
 \arguments{
 \item{spe}{a \link[SpatialExperiment:SpatialExperiment]{SpatialExperiment}}
@@ -30,7 +30,7 @@ if (enough_ram()) {
     spe_qc$in_tissue[spe_qc$array_col < 10] <- FALSE
 
     ## adds QC metrics to colData of the spe
-    spe_qc <- metrics_qc(spe_qc)
+    spe_qc <- add_qc_metrics(spe_qc)
     colData(spe_qc)
 
     ## visualize edge spots