ran styler

R/getSubnetworkFromIndra.R

@@ -1,9 +1,9 @@
 #' Get subnetwork from INDRA database
-#' 
+#'
 #' Using differential abundance results from MSstats, this function retrieves
 #' a subnetwork of protein interactions from INDRA database.
 #'
-#' @param input output of groupComparison function's comparisionResult table, 
+#' @param input output of groupComparison function's comparisionResult table,
 #' which contains a list of proteins and their corresponding p-values, logFCs,
 #' along with additional HGNC ID and HGNC name columns
 #' @param pvalueCutoff p-value cutoff for filtering. Default is NULL, i.e. no

R/visualizeNetworks.R

@@ -1,13 +1,13 @@
 #' Create visualization of network
-#' 
-#' Use results from INDRA to generate a visualization of the a network on 
-#' Cytoscape Desktop.  Note that the Cytoscape Desktop app must be open for 
+#'
+#' Use results from INDRA to generate a visualization of the a network on
+#' Cytoscape Desktop.  Note that the Cytoscape Desktop app must be open for
 #' this function to work.
 #'
-#' @param nodes dataframe of nodes consisting of columns 
+#' @param nodes dataframe of nodes consisting of columns
 #' id (chararacter), pvalue (number), logFC (number)
 #' @param edges dataframe of edges consisting of columns
-#' source (character), target (character), interaction (character), 
+#' source (character), target (character), interaction (character),
 #' evidenceCount (number), evidenceLink (character)
 #' @param pvalueCutoff p-value cutoff for coloring significant proteins.
 #' Default is 0.05

tests/testthat/test-getSubnetworkFromIndra.R

@@ -18,7 +18,8 @@ test_that("getSubnetworkFromIndra with pvalue filter works correctly", {
         return(readRDS(system.file("extdata/indraResponse.rds", package = "MSstatsBioNet")))
     })
     suppressWarnings(
-        subnetwork <- getSubnetworkFromIndra(input, pvalueCutoff = 0.45))
+        subnetwork <- getSubnetworkFromIndra(input, pvalueCutoff = 0.45)
+    )
     expect_equal(nrow(subnetwork$nodes), 6)
     expect_equal(nrow(subnetwork$edges), 2)
 })

tests/testthat/test-visualizeNetworks.R

@@ -85,16 +85,16 @@ test_that("visualizeNetworks with p-value and logFC constraints works", {
 
 test_that("visualizeNetworks returns warning for non-interactive calls", {
     input <- readRDS(system.file("extdata/subnetwork.rds",
-                                 package = "MSstatsBioNet"
+        package = "MSstatsBioNet"
     ))
-    
+
     mock_interactive <- mock(FALSE)
     stub(
         visualizeNetworks, "interactive",
         mock_interactive
     )
-    
+
     expect_warning(visualizeNetworks(input$nodes, input$edges,
-                                    pvalueCutoff = 0.01, logfcCutoff = 2.5
+        pvalueCutoff = 0.01, logfcCutoff = 2.5
     ))
 })

vignettes/MSstatsBioNet.Rmd

@@ -22,8 +22,9 @@ knitr::opts_chunk$set(
 Run this code below to install MSstatsBioNet from bioconductor
 
 ```{r eval = FALSE}
-if (!require("BiocManager", quietly = TRUE))
+if (!require("BiocManager", quietly = TRUE)) {
     install.packages("BiocManager")
+}
 
 BiocManager::install("MSstatsBioNet")
 ```