From 67206617f111aa20fa8fce5e039e2e2a37545d0c Mon Sep 17 00:00:00 2001
From: Christian Hohenfeld <r@hohenfeld.is>
Date: Wed, 4 Aug 2021 11:52:08 +0200
Subject: [PATCH] Add function for creating subgraphs.
---
DESCRIPTION | 2 +-
NAMESPACE | 1 +
R/to_subgraph.R | 23 +++++++++++++++++++++++
man/to_subgraph.Rd | 21 +++++++++++++++++++++
tests/testthat/test-to_subgraph.R | 9 +++++++++
5 files changed, 55 insertions(+), 1 deletion(-)
create mode 100644 R/to_subgraph.R
create mode 100644 man/to_subgraph.Rd
create mode 100644 tests/testthat/test-to_subgraph.R
diff --git a/DESCRIPTION b/DESCRIPTION
index e386038..3cf4ce8 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
Package: rsAnalysis
Title: High-Level Tools for rsfMRI analysis
-Version: 0.4.1
+Version: 0.4.2
Authors@R:
person(given = "Christian",
family = "Hohenfeld",
diff --git a/NAMESPACE b/NAMESPACE
index 644fcb9..e87f8b3 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -25,6 +25,7 @@ export(remove_loops)
export(rs_pipeline)
export(single_component_threshold)
export(split_graph_list)
+export(to_subgraph)
importFrom(magrittr,"%>%")
importFrom(rlang,":=")
importFrom(rlang,.data)
diff --git a/R/to_subgraph.R b/R/to_subgraph.R
new file mode 100644
index 0000000..80715af
--- /dev/null
+++ b/R/to_subgraph.R
@@ -0,0 +1,23 @@
+#' Take a list of graphs and return subgraphs.
+#'
+#' `to_subgraph` makes the assumption that all graphs share a common set of
+#' nodes like it is common with graph analysis of the brain.
+#'
+#' @param graph_list A list of tbl_graphs
+#' @param to_keep The names of the nodes to keep.
+#'
+#' @return A list of the graphs in `graph_list` reduced to the respective
+#' subgraphs.
+#' @export
+to_subgraph <- function(graph_list, to_keep) {
+ all_nodes <- graph_list[[1]] %>%
+ tidygraph::activate("nodes") %>%
+ tibble::as_tibble() %>%
+ tibble::deframe()
+
+ to_remove_net <- all_nodes[!all_nodes %in% to_keep]
+ graph_list <- lapply(graph_list,
+ function(x) igraph::delete.vertices(x, to_remove_net))
+ graph_list <- lapply(graph_list, tidygraph::as_tbl_graph)
+ graph_list
+}
diff --git a/man/to_subgraph.Rd b/man/to_subgraph.Rd
new file mode 100644
index 0000000..0c71cc4
--- /dev/null
+++ b/man/to_subgraph.Rd
@@ -0,0 +1,21 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/to_subgraph.R
+\name{to_subgraph}
+\alias{to_subgraph}
+\title{Take a list of graphs and return subgraphs.}
+\usage{
+to_subgraph(graph_list, to_keep)
+}
+\arguments{
+\item{graph_list}{A list of tbl_graphs}
+
+\item{to_keep}{The names of the nodes to keep.}
+}
+\value{
+A list of the graphs in `graph_list` reduced to the respective
+subgraphs.
+}
+\description{
+`to_subgraph` makes the assumption that all graphs share a common set of
+nodes like it is common with graph analysis of the brain.
+}
diff --git a/tests/testthat/test-to_subgraph.R b/tests/testthat/test-to_subgraph.R
new file mode 100644
index 0000000..daecd32
--- /dev/null
+++ b/tests/testthat/test-to_subgraph.R
@@ -0,0 +1,9 @@
+describe("to_subgraph", {
+ data("graph_list")
+ it("creates a graph only containing the specified nodes", {
+ to_keep <- c("Precentral_L", "Precentral_R")
+ sub_list <- to_subgraph(graph_list, to_keep)
+ sub_order <- sapply(sub_list, igraph::gorder, USE.NAMES = FALSE)
+ expect_true(all(sub_order == length(to_keep)))
+ })
+})
--
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