Post-review changes (#28)

* Remove seed setting from start of vignette

* Include package loading chunk in vignette

* Make WGCNA picksoftthreshold silent

* Fix application of capture.output for WGCNA soft thresholding function

* Import capture.output from utils

* Add capture.output to NAMESPACE

* Improve stability plot resolution

* Bump version

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: ReducedExperiment
 Type: Package
 Title: Containers and tools for dimensionally-reduced -omics representations
-Version: 0.99.4
+Version: 0.99.5
 Authors@R: c(
     person("Jack", "Gisby", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0003-0511-8123")),

NAMESPACE

@@ -90,3 +90,4 @@ importClassesFrom(SummarizedExperiment,SummarizedExperiment)
 importFrom(lme4,lmerControl)
 importFrom(lmerTest,lmer)
 importFrom(utils,.DollarNames)
+importFrom(utils,capture.output)

NEWS.md

@@ -1,3 +1,9 @@
+# ReducedExperiment 0.99.5 (2025-01-09)
+* Switched variable names to CamelCase
+* Added comparison of ReducedExperiment and similar object systems
+* Ensured methods are replicable with seed arguments
+* Passed Bioconductor review
+
 # ReducedExperiment 0.99.0 (2024-09-27)
 * Developed ReducedExperiment classes and functionality
 * Made package compatible with R and BioC checks

R/modules.R

@@ -195,6 +195,7 @@ identifyModules <- function(
 #'
 #' @author Jack Gisby
 #'
+#' @importFrom utils capture.output
 #' @export
 assessSoftThreshold <- function(
     X, assay_name = "normal", powerVector = 1:30, RsquaredCut = 0.85,
@@ -207,14 +208,27 @@ assessSoftThreshold <- function(
     if (inherits(X, "SummarizedExperiment"))
         X <- assay(X, assay_name)
 
-    # Apply soft thresholding function
-    threshold_output <- WGCNA::pickSoftThreshold(
-        t(X),
-        powerVector = powerVector, RsquaredCut = RsquaredCut,
-        corFnc = corFnc, networkType = networkType,
-        blockSize = maxBlockSize, verbose = verbose, ...
+    args <- list(
+        data = t(X),
+        powerVector = powerVector,
+        RsquaredCut = RsquaredCut,
+        corFnc = corFnc,
+        networkType = networkType,
+        blockSize = maxBlockSize,
+        verbose = verbose,
+        ...
     )
 
+    # Apply soft thresholding function (if verbose == 0 suppress the print)
+    if (verbose == 0) {
+        capture.output(
+            threshold_output <- do.call(WGCNA::pickSoftThreshold, args),
+            file = NULL
+        )
+    } else {
+        threshold_output <- do.call(WGCNA::pickSoftThreshold, args)
+    }
+
     # Get the output
     wgcna_power_estimate <- threshold_output$powerEstimate
     fit_indices <- threshold_output$fitIndices

vignettes/ReducedExperiment.Rmd

@@ -24,9 +24,6 @@ knitr::opts_chunk$set(
   fig.align = "center",
   dpi = 300
 )
-
-# Seed
-set.seed(1)
 ```
 
 # Installation
@@ -53,7 +50,7 @@ devtools::install_github("jackgisby/ReducedExperiment")
 
 # Introduction
 
-```{r load-packages, message=FALSE, warning=FALSE, include=FALSE}
+```{r load-packages, message=FALSE, warning=FALSE, include=TRUE}
 library(SummarizedExperiment)
 library(ReducedExperiment)
 library(ggplot2)