From 1af3c5e314eb05f6cfe99cbb63ada22f77541b4c Mon Sep 17 00:00:00 2001
From: tonywu1999 <wu.anthon@northeastern.edu>
Date: Wed, 6 Nov 2024 12:02:46 -0500
Subject: [PATCH] docs(getSubnetworkFromIndra): Switch MSstats as dependency,
 adjust link to groupComparison (#22)

* docs(getSubnetworkFromIndra): Switch MSstats as dependency, add link to groupComparison

* update manual for visualizeNetworks
---
 DESCRIPTION                   |  4 ++--
 R/getSubnetworkFromIndra.R    |  8 ++++----
 man/getSubnetworkFromIndra.Rd | 10 ++++------
 man/visualizeNetworks.Rd      |  8 ++++----
 4 files changed, 14 insertions(+), 16 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 8105f73..c34fdd8 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -20,7 +20,8 @@ Imports:
     RCy3,
     httr,
     jsonlite,
-    r2r
+    r2r,
+    MSstats
 Suggests: 
     data.table,
     BiocStyle,
@@ -28,7 +29,6 @@ Suggests:
     rmarkdown,
     testthat (>= 3.0.0),
     mockery,
-    MSstats,
     MSstatsConvert
 VignetteBuilder: knitr
 biocViews: ImmunoOncology, MassSpectrometry, Proteomics, Software, 
diff --git a/R/getSubnetworkFromIndra.R b/R/getSubnetworkFromIndra.R
index 4d60492..7c20dda 100644
--- a/R/getSubnetworkFromIndra.R
+++ b/R/getSubnetworkFromIndra.R
@@ -3,14 +3,14 @@
 #' 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,
-#' which contains a list of proteins and their corresponding p-values, logFCs,
-#' along with additional HGNC ID and HGNC name columns
+#' @param input output of \code{\link[MSstats]{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
 #' filtering
 #'
 #' @return list of 2 data.frames, nodes and edges
-#' @seealso \code{\link[MSstats]{groupComparison}}
 #'
 #' @export
 #'
diff --git a/man/getSubnetworkFromIndra.Rd b/man/getSubnetworkFromIndra.Rd
index ad45434..2f5ed5b 100644
--- a/man/getSubnetworkFromIndra.Rd
+++ b/man/getSubnetworkFromIndra.Rd
@@ -7,9 +7,10 @@
 getSubnetworkFromIndra(input, pvalueCutoff = NULL)
 }
 \arguments{
-\item{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}
+\item{input}{output of \code{\link[MSstats]{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}
 
 \item{pvalueCutoff}{p-value cutoff for filtering. Default is NULL, i.e. no
 filtering}
@@ -31,6 +32,3 @@ head(subnetwork$nodes)
 head(subnetwork$edges)
 
 }
-\seealso{
-\code{\link[MSstats]{groupComparison}}
-}
diff --git a/man/visualizeNetworks.Rd b/man/visualizeNetworks.Rd
index 07afb62..dfe3eaf 100644
--- a/man/visualizeNetworks.Rd
+++ b/man/visualizeNetworks.Rd
@@ -7,11 +7,11 @@
 visualizeNetworks(nodes, edges, pvalueCutoff = 0.05, logfcCutoff = 0.5)
 }
 \arguments{
-\item{nodes}{dataframe of nodes consisting of columns 
+\item{nodes}{dataframe of nodes consisting of columns
 id (chararacter), pvalue (number), logFC (number)}
 
 \item{edges}{dataframe of edges consisting of columns
-source (character), target (character), interaction (character), 
+source (character), target (character), interaction (character),
 evidenceCount (number), evidenceLink (character)}
 
 \item{pvalueCutoff}{p-value cutoff for coloring significant proteins.
@@ -24,8 +24,8 @@ proteins. Default is 0.5}
 cytoscape visualization of subnetwork
 }
 \description{
-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.
 }
 \examples{