Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Layouts #245

Merged
merged 4 commits into from
Feb 22, 2024
Merged

Layouts #245

Show file tree
Hide file tree
Changes from 3 commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
7d3fc85
draft layouts
d-callan Feb 16, 2024
5995085
update tests
d-callan Feb 16, 2024
108d566
update Node toJSON
d-callan Feb 16, 2024
c40ec2c
Merge branch 'main' into layouts
d-callan Feb 22, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion R/class-KPartiteNetwork.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -137,7 +137,7 @@ setMethod("KPartiteNetwork", signature("data.frame", "missing", "missing"), func
variables = VariableMetadataList(),
...
) {
new("KPartiteNetwork", links=LinkList(object), nodes=NodeList(object), partitions=partitions, linkColorScheme=linkColorScheme, variableMapping=variables)
new("KPartiteNetwork", links=LinkList(object), nodes=NodeList(object, layout='none'), partitions=partitions, linkColorScheme=linkColorScheme, variableMapping=variables)
})

#' @export
Expand Down
9 changes: 7 additions & 2 deletions R/class-Network.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -64,7 +64,10 @@ setClass("Network",
#' @param links LinkList
#' @param nodes NodeList
#' @param object Object containing data to be converted to a Network
#' @param linkColorScheme string defining the type of coloring scheme the links follow. Options are 'none' (default) and 'posneg'.
#' @param linkColorScheme string defining the type of coloring scheme the links follow.
#' Options are 'none' (default) and 'posneg'.
#' @param layout string defining the layout of the network. Options are 'force', 'circle',
d-callan marked this conversation as resolved.
Show resolved Hide resolved
#' and 'nicely' which are implemented in igraph. Default is 'nicely'.
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

suggestion - anything other than "nicely" for the default. "Nicely" isn't descriptive at all haha. I don't know what "nicely" means other than i expect it looks nice :) I think it'd be more helpful to see something plain but readable (such as "circle") and then choose a layout from more complicated options.

Copy link
Contributor Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

nice is a nice option though. it goes through different algorithms i dont remember based on some network metrics i dont remember. and as the default, people dont have to ask for nicely, or ever see thats what its called. they just get it by default, and can ask for specific things by name. i cant imagine ever asking for a thing called nicely without knowing what it was..

#' @param variables VariableMetadataList
#' @return Network
#' @export
Expand Down Expand Up @@ -100,10 +103,12 @@ setMethod("Network", signature("data.frame", "missing", "missing"), function(
links,
nodes,
linkColorScheme = 'none',
layout = c("nicely", "force", "circle"),
d-callan marked this conversation as resolved.
Show resolved Hide resolved
variables = VariableMetadataList(),
...
) {
new("Network", links=LinkList(object, linkColorScheme), nodes=NodeList(object), linkColorScheme=linkColorScheme, variableMapping=variables)
layout <- veupathUtils::matchArg(layout)
new("Network", links=LinkList(object, linkColorScheme), nodes=NodeList(object, layout), linkColorScheme=linkColorScheme, variableMapping=variables)
})

#' @export
Expand Down
31 changes: 25 additions & 6 deletions R/constructors-Node.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -133,25 +133,44 @@ setMethod("Node", "missing", function(id, x = numeric(), y = numeric(), color =
#'
#' Generate a NodeList from an edgeList
#' @param object Object containing data to be converted to a NodeList
#' @param layout string indicating the layout algorithm to be used. Options are 'none', 'force',
#' 'circle' or 'nicely' which are implemented via igraph. Defaults to 'nicely'.
#' @return NodeList
#' @export
#' @examples
#' NodeList(data.frame(source='a',target='b'))
setGeneric("NodeList", function(object) standardGeneric("NodeList"))
setGeneric("NodeList", function(object, ...) standardGeneric("NodeList"))

#' @export
setMethod("NodeList", "data.frame", function(object = data.frame(source=character(),target=character())) {
setMethod("NodeList", "data.frame", function(object = data.frame(source=character(),target=character()), layout = c("nicely", "force", "circle", "none")) {
if (!inherits(isValidEdgeList(object), "logical")) {
stop(paste("Invalid edgeList:", isValidEdgeList(object), collapse = '\n'))
}
layout <- veupathUtils::matchArg(layout)

allNodeIds <- c(object$source, object$target)
graph <- igraph::graph_from_data_frame(object, directed = FALSE)
if (layout != "none") {
if (layout == "force") {
coords <- igraph::layout_with_fr(graph)
} else if (layout == "circle") {
coords <- igraph::layout_in_circle(graph)
} else if (layout == "nicely") {
coords <- igraph::layout_nicely(graph)
} else {
stop("layout must be 'force', 'circle' or 'nicely'")
}
rownames(coords) <- names(igraph::V(graph))
}

makeNodeWithDegree <- function(nodeId, allNodeIds) {
new("Node", id = NodeId(nodeId), degree = length(which(allNodeIds == nodeId)))
# if we want to move this out of the constructor it needs to have graph and coords passed to it
d-callan marked this conversation as resolved.
Show resolved Hide resolved
makeNodeWithDegreeAndLayout <- function(nodeId) {
x <- ifelse(layout != "none", coords[nodeId, 1], numeric())
y <- ifelse(layout != "none", coords[nodeId, 2], numeric())
degree <- igraph::degree(graph, v = nodeId, mode = "all")
new("Node", id = NodeId(nodeId), degree = unname(degree), x = x, y = y)
}

nodesList <- lapply(unique(allNodeIds), makeNodeWithDegree, allNodeIds)
nodesList <- lapply(names(igraph::V(graph)), makeNodeWithDegreeAndLayout)
new("NodeList", nodesList)
})

Expand Down
1 change: 1 addition & 0 deletions R/methods-Network.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -12,6 +12,7 @@ setMethod("getLinkColorScheme", "Network", function(object) object@linkColorSche
# No setters! Once created, a network should only be updated via network methods

setMethod("getDegrees", "Network", function(object) getDegrees(getNodes(object)))
setMethod("getCoords", "Network", function(object) getCoords(getNodes(object)))

## General network methods

Expand Down
12 changes: 10 additions & 2 deletions R/methods-Nodes.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -42,6 +42,14 @@ setMethod("getWeights", "NodeList", function(object) unlist(lapply(as.list(objec
setMethod("getColors", "NodeList", function(object) unlist(lapply(as.list(object), color)))
setGeneric("getDegrees", function(object) standardGeneric("getDegrees"))
setMethod("getDegrees", "NodeList", function(object) unlist(lapply(as.list(object), degree)))
setGeneric("getCoords", function(object) standardGeneric("getCoords"))
setMethod("getCoords", "NodeList", function(object) {
coords <- data.frame(x = unlist(lapply(as.list(object), x)), y = unlist(lapply(as.list(object), y)))
d-callan marked this conversation as resolved.
Show resolved Hide resolved
if (nrow(coords) == 0 || all(is.na(coords))) {
return(NULL)
}
return(coords)
})

## Methods for NodeIdList
setMethod("getNodeIds", "NodeIdList", function(object) unlist(lapply(as.list(object), id)))
Expand All @@ -60,8 +68,8 @@ setMethod(toJSONGeneric, "Node", function(object, named = c(FALSE, TRUE)) {
tmp <- character()

tmp <- paste0('"id":', jsonlite::toJSON(jsonlite::unbox(id(object))))
if (!!length(x(object))) tmp <- paste0(tmp, ',"x":', jsonlite::toJSON(jsonlite::unbox(x(object))))
if (!!length(y(object))) tmp <- paste0(tmp, ',"y":', jsonlite::toJSON(jsonlite::unbox(y(object))))
if (!!length(x(object)) && !is.na(x(object))) tmp <- paste0(tmp, ',"x":', jsonlite::toJSON(jsonlite::unbox(x(object))))
if (!!length(y(object)) && !is.na(y(object))) tmp <- paste0(tmp, ',"y":', jsonlite::toJSON(jsonlite::unbox(y(object))))
if (!!length(color(object))) tmp <- paste0(tmp, ',"color":', jsonlite::toJSON(jsonlite::unbox(color(object))))
if (!!length(weight(object))) tmp <- paste0(tmp, ',"weight":', jsonlite::toJSON(jsonlite::unbox(weight(object))))
if (!!length(degree(object))) tmp <- paste0(tmp, ',"degree":', jsonlite::toJSON(jsonlite::unbox(degree(object))))
Expand Down
4 changes: 3 additions & 1 deletion tests/testthat/test-kpartite-network.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -166,7 +166,9 @@ test_that("we can build a KPartiteNetwork from an edgeList data.frame", {
))
)

expect_equal(getNodes(net), NodeList(c(Node('a', degree=2), Node('b', degree=2), Node('c', degree=1), Node('d', degree=1))))
expect_equal(getNodeIds(net), c('a', 'b', 'c', 'd'))
expect_equal(getDegrees(net), c(2, 2, 1, 1))
expect_equal(getCoords(net), NULL)
expect_equal(getLinks(net), LinkList(c(Link(source = Node('a'), target = Node('b')), Link(source = Node('b'), target = Node('a')), Link(source = Node('c'), target = Node('d')))))
expect_equal(partitions(net), Partitions(list(Partition(list(Node('a'), Node('c'))), Partition(list(Node('b'), Node('d'))))))
expect_equal(getLinkColorScheme(net), 'none')
Expand Down
12 changes: 9 additions & 3 deletions tests/testthat/test-network.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -183,7 +183,9 @@ test_that("we can build a Network from an edgeList data.frame", {
target = c('b', 'c', 'a')
)
net <- Network(object = edgeList)
expect_equal(getNodes(net), NodeList(c(Node('a', degree=2), Node('b', degree=2), Node('c', degree=2))))
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(getLinks(net)[[1]]@source, NodeId('a'))
expect_equal(getLinks(net)[[1]]@target, NodeId('b'))
expect_equal(getLinks(net)[[2]]@source, NodeId('b'))
Expand All @@ -200,7 +202,9 @@ test_that("we can build a Network from an edgeList data.frame", {
weight = c(1,2,3)
)
net <- Network(object = edgeList)
expect_equal(getNodes(net), NodeList(c(Node('a', degree=2), Node('b', degree=2), Node('c', degree=2))))
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(getLinks(net)[[2]]@weight, 2)
expect_equal(getLinks(net)[[3]]@weight, 3)
expect_equal(getLinkColorScheme(net), 'none')
Expand All @@ -213,7 +217,9 @@ test_that("we can build a Network from an edgeList data.frame", {
weight = c(-10,0,10)
)
net <- Network(object = edgeList, linkColorScheme = 'posneg')
expect_equal(getNodes(net), NodeList(c(Node('a', degree=2), Node('b', degree=2), Node('c', degree=2))))
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(getLinks(net)[[1]]@weight, -10)
expect_equal(getLinks(net)[[2]]@weight, 0)
expect_equal(getLinks(net)[[3]]@weight, 10)
Expand Down