change pValueThreshold default to NULL

VEuPathDB · Apr 26, 2024 · 1952847 · 1952847
1 parent 542411e
commit 1952847
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Showing 4 changed files with 28 additions and 26 deletions.
diff --git a/R/class-CorrelationLink.R b/R/class-CorrelationLink.R
@@ -183,7 +183,7 @@ setClass("CorrelationLinkList",
 #' @param linkColorScheme Either 'none' or 'posneg'. If 'posneg', the link color will be based on the sign of the correlation coefficient.
 #' @param correlationCoefThreshold numeric value used to filter links based on correlationCoef. Default is NULL (i.e. no filtering).
 #' Any links with an absolute correlationCoef below this threshold will be removed.
-#' @param pValueThreshold numeric value used to filter links based on pValue. Default is 0.05.
+#' @param pValueThreshold numeric value used to filter links based on pValue. Default is NULL (i.e. no filtering).
 #' Any links with an pValue above this threshold will be removed.
 #' @return CorrelationLinkList
 #' @export
@@ -195,7 +195,7 @@ function(
   object, 
   linkColorScheme = c('none', 'posneg'),
   correlationCoefThreshold = NULL,
-  pValueThreshold = 0.05  
+  pValueThreshold = NULL 
 ) standardGeneric("CorrelationLinkList"), signature = c("object"))
 
 #' @rdname CorrelationLinkList
@@ -210,7 +210,7 @@ function(
   ), 
   linkColorScheme = c('none', 'posneg'),
   correlationCoefThreshold = NULL,
-  pValueThreshold = 0.05
+  pValueThreshold = NULL
 ) {
   linkColorScheme <- veupathUtils::matchArg(linkColorScheme)
 

diff --git a/R/class-CorrelationNetwork.R b/R/class-CorrelationNetwork.R
@@ -40,7 +40,7 @@ check_correlation_network <- function(object) {
 #' @slot variableMapping veupathUtils::VariableMetadataList object defining the variable mappings in the network.
 #' @slot correlationCoefThreshold numeric defining the correlation coefficient threshold for filtering links. Default is NA (no filtering).
 #' Any link with an absolute correlation coefficient below this threshold will be filtered out.
-#' @slot pValueThreshold numeric defining the p-value threshold for filtering links. Default is 0.05.
+#' @slot pValueThreshold numeric defining the p-value threshold for filtering links. Default is NA (no filtering).
 #' Any link with an p-value above this threshold will be filtered out. 
 #' @name CorrelationNetwork-class
 #' @rdname CorrelationNetwork-class
@@ -58,7 +58,7 @@ setClass("CorrelationNetwork",
     nodes = NodeList(),
     linkColorScheme = 'posneg', #change default from base Network's 'none'
     correlationCoefThreshold = NA_real_,
-    pValueThreshold = 0.05,
+    pValueThreshold = NA_real_,
     variableMapping = VariableMetadataList()
   ),
   validity = check_correlation_network
@@ -74,7 +74,7 @@ setClass("CorrelationNetwork",
 #' @param object Object containing data to be converted to a Network
 #' @param correlationCoefThreshold numeric defining the correlation coefficient threshold for filtering links. Default is NULL (no filtering).
 #' Any link with an absolute correlation coefficient below this threshold will be filtered out.
-#' @param pValueThreshold numeric defining the p-value threshold for filtering links. Default is 0.05.
+#' @param pValueThreshold numeric defining the p-value threshold for filtering links. Default is NULL (no filtering).
 #' Any link with an p-value above this threshold will be filtered out.
 #' @param linkColorScheme string defining the type of coloring scheme the links follow. 
 #' Options are 'none' and 'posneg' (default).
@@ -93,7 +93,7 @@ setGeneric("CorrelationNetwork",
     links,
     nodes,
     correlationCoefThreshold = NULL,
-    pValueThreshold = 0.05,
+    pValueThreshold = NULL,
     linkColorScheme = 'posneg',
     variables = VariableMetadataList(),
     ...
@@ -108,7 +108,7 @@ setMethod("CorrelationNetwork", signature("missing", "CorrelationLinkList", "Nod
   links,
   nodes,
   correlationCoefThreshold = NULL,
-  pValueThreshold = 0.05,
+  pValueThreshold = NULL,
   linkColorScheme = 'posneg', 
   variables = VariableMetadataList(),
   pruneIsolatedNodes = c(TRUE, FALSE)
@@ -139,7 +139,7 @@ setMethod("CorrelationNetwork", signature("data.frame", "missing", "missing"), f
   links, 
   nodes,
   correlationCoefThreshold = NULL,
-  pValueThreshold = 0.05,
+  pValueThreshold = NULL,
   linkColorScheme = 'posneg', 
   layout = c("nicely", "force", "circle"),
   variables = VariableMetadataList(), 
@@ -172,7 +172,7 @@ setMethod("CorrelationNetwork", signature("missing", "missing", "missing"), func
   links, 
   nodes,
   correlationCoefThreshold = NULL,
-  pValueThreshold = 0.05,
+  pValueThreshold = NULL,
   linkColorScheme = 'none', 
   variables = VariableMetadataList(), 
   ...

diff --git a/R/methods-CorrelationLinks.R b/R/methods-CorrelationLinks.R
@@ -29,7 +29,7 @@ setMethod("getPValues", "CorrelationLinkList", function(object) unlist(lapply(ob
 #' @param object CorrelationLinkList or CorrelationNetwork
 #' @param correlationCoefThreshold threshold to filter edges by correlation coefficient. Default is NULL.
 #' Any links with absolute correlation coefficients below this threshold will be removed.
-#' @param pValueThreshold threshold to filter edges by p-value. Default is 0.05.
+#' @param pValueThreshold threshold to filter edges by p-value. Default is NULL.
 #' Any links with p-values above this threshold will be removed.
 #' @param verbose boolean indicating if timed logging is desired
 #' @return CorrelationLinkList or CorrelationNetwork
@@ -39,7 +39,7 @@ setGeneric("pruneCorrelationLinks",
 function(
     object, 
     correlationCoefThreshold = NULL,
-    pValueThreshold = 0.05, 
+    pValueThreshold = NULL, 
     verbose = c(TRUE, FALSE)
 ) {
     standardGeneric("pruneCorrelationLinks")
@@ -51,7 +51,7 @@ setMethod("pruneCorrelationLinks", "CorrelationLinkList",
 function(
     object, 
     correlationCoefThreshold = NULL,
-    pValueThreshold = 0.05,
+    pValueThreshold = NULL,
     verbose = c(TRUE, FALSE)
 ) {
     verbose <- veupathUtils::matchArg(verbose)

diff --git a/tests/testthat/test-correlation-network.R b/tests/testthat/test-correlation-network.R
@@ -16,7 +16,11 @@ test_that("correlation networks can be created", {
     link3 <- CorrelationLink(source = nodeC, target = nodeA, correlationCoef = -.8, pValue = .1)
 
     # Create a network
-    net <- CorrelationNetwork(links = CorrelationLinkList(c(link1, link2, link3)), nodes = NodeList(c(nodeA, nodeB, nodeC)))
+    net <- CorrelationNetwork(
+        links = CorrelationLinkList(c(link1, link2, link3)), 
+        nodes = NodeList(c(nodeA, nodeB, nodeC)),
+        pValueThreshold = .05
+    )
 
     expect_equal(getNodes(net), NodeList(c(nodeA, nodeB, nodeC)))
     expect_equal(getLinks(net), CorrelationLinkList(c(link1, link2))) ## link 3 is pruned for high pValue
@@ -25,8 +29,7 @@ test_that("correlation networks can be created", {
     # Create a network
     net <- CorrelationNetwork(
         links = CorrelationLinkList(c(link1, link2, link3)), 
-        nodes = NodeList(c(nodeA, nodeB, nodeC)),
-        pValueThreshold = NULL
+        nodes = NodeList(c(nodeA, nodeB, nodeC))
     )
 
     expect_equal(getNodes(net), NodeList(c(nodeA, nodeB, nodeC)))
@@ -89,8 +92,7 @@ test_that("correlation networks can be pruned by threshold", {
     # Create a network
     net <- CorrelationNetwork(
         links = CorrelationLinkList(c(link1, link2, link3)), 
-        nodes = NodeList(c(nodeA, nodeB, nodeC)),
-        pValueThreshold = NULL
+        nodes = NodeList(c(nodeA, nodeB, nodeC))
     )
 
     net <- pruneCorrelationLinks(net, pValueThreshold = .05)
@@ -124,8 +126,7 @@ test_that("toJSON works for networks", {
     # Create a network
     net <- CorrelationNetwork(
         links = CorrelationLinkList(c(link1, link2, link3)), 
-        nodes = NodeList(c(nodeA, nodeB, nodeC)), 
-        pValueThreshold = NULL
+        nodes = NodeList(c(nodeA, nodeB, nodeC))
     )
 
     # Convert to JSON
@@ -142,7 +143,8 @@ test_that("toJSON works for networks", {
 
     net <- CorrelationNetwork(
         links = CorrelationLinkList(c(link1, link2, link3)), 
-        nodes = NodeList(c(nodeA, nodeB, nodeC))
+        nodes = NodeList(c(nodeA, nodeB, nodeC)),
+        pValueThreshold = .05
     )
 
     json <- veupathUtils::toJSON(net)
@@ -165,7 +167,7 @@ test_that("we can build a Network from an edgeList data.frame", {
         correlationCoef = c(.8,.3,-.8),
         pValue = c(.01,.001,.1)
     )
-    net <- CorrelationNetwork(object = edgeList, linkColorScheme = 'none', pValueThreshold = NULL)
+    net <- CorrelationNetwork(object = edgeList, linkColorScheme = 'none')
     expect_equal(getNodeIds(net), c('a', 'b', 'c'))
     expect_equal(getDegrees(net), c(2, 2, 2))
     expect_equal(!is.null(getCoords(net)), TRUE)
@@ -181,7 +183,7 @@ test_that("we can build a Network from an edgeList data.frame", {
         correlationCoef = c(.8,.3,-.8),
         pValue = c(.01,.001,.1)
     )
-    net <- CorrelationNetwork(object = edgeList, linkColorScheme = 'posneg', pValueThreshold = NULL)
+    net <- CorrelationNetwork(object = edgeList, linkColorScheme = 'posneg')
     expect_equal(getNodeIds(net), c('a', 'b', 'c'))
     expect_equal(getDegrees(net), c(2, 2, 2))
     expect_equal(!is.null(getCoords(net)), TRUE)
@@ -201,7 +203,7 @@ test_that("we can build a Network from an edgeList data.frame", {
         correlationCoef = c(.8,.3,-.8),
         pValue = c(.01,.001,.1)
     )
-    net <- CorrelationNetwork(object = edgeList)
+    net <- CorrelationNetwork(object = edgeList, pValueThreshold = .05)
     expect_equal(getNodeIds(net), c('a', 'b', 'c'))
     expect_equal(getDegrees(net), c(2, 2, 2))
     expect_equal(!is.null(getCoords(net)), TRUE)
@@ -217,12 +219,12 @@ test_that("we can build a Network from an edgeList data.frame", {
         correlationCoef = c(.8,.3,-.8),
         pValue = c(.01,.001,.1)
     )
-    net <- CorrelationNetwork(object = edgeList, correlationCoefThreshold = .5, pValueThreshold = NULL)
+    net <- CorrelationNetwork(object = edgeList, correlationCoefThreshold = .5)
     expect_equal(getNodeIds(net), c('a', 'b', 'c'))
     expect_equal(getDegrees(net), c(2, 2, 2))
     expect_equal(!is.null(getCoords(net)), TRUE)
     expect_equal(getLinkColorScheme(net), 'posneg')
     expect_equal(length(getLinks(net)), 2)
     expect_equal(getLinks(net)[[1]]@weight, .8)
-    expect_equal(getLinks(net)[[2]]@weight, .8) #second link is actually third link!!
+    expect_equal(getLinks(net)[[2]]@weight, .8) #second link is actually third link bc of correlationCoefThreshold!!
 })