# ==============================================================================
# Functions for retrieving current values for visual properties.
#
# I. General functions for getting node, edge and network properties
# II. Specific functions for getting particular node, edge and network properties
#
# ==============================================================================
# I. General Functions
# ------------------------------------------------------------------------------
#' @title Get Node Property Values
#'
#' @description Get values for any node property of the specified nodes.
#' @param node.names List of node names or SUIDs. Default is NULL for all
#' nodes.
#' @param visual.property Name of a visual property. See \link{getVisualPropertyNames}.
#' @param network (optional) Name or SUID of the network. Default is the "current" network active in Cytoscape.
#' @param base.url (optional) Ignore unless you need to specify a custom domain,
#' port or version to connect to the CyREST API. Default is http://localhost:1234
#' and the latest version of the CyREST API supported by this version of RCy3.
#' @details This method retrieves the actual property of the node, given the
#' current visual style, factoring together any default, mapping and bypass setting.
#' @return Named list of property values
#' @examples \donttest{
#' getNodeProperty(c('node 0','node 1'),'NODE_SHAPE')
#' }
#' @export
getNodeProperty <- function(node.names = NULL,
visual.property,
network = NULL,
base.url = .defaultBaseUrl) {
net.SUID <- getNetworkSuid(network,base.url)
net.views.SUIDs <- getNetworkViews(net.SUID, base.url)
view.SUID <- as.character(net.views.SUIDs[[1]])
if (is.null(node.names)){
res <- cyrestGET(paste("networks",
net.SUID,
"views",
view.SUID,
"nodes",
sep = "/"),
c(visualProperty=visual.property),
base.url = base.url)
node.suids <- unlist(lapply(res, function(x) x$SUID))
node.props <- unlist(lapply(res, function(x) unlist(x$view)['value']))
node.props <- setNames(node.props,.nodeSUIDToNodeName(node.suids))
return(node.props)
} else {
node.SUIDs <-
.nodeNameToNodeSUID(node.names, net.SUID, base.url)
node.props <- c()
for (i in seq_len(length(node.SUIDs))) {
node.SUID <- as.character(node.SUIDs[i])
res <- cyrestGET(paste("networks",
net.SUID,
"views",
view.SUID,
"nodes",
node.SUID,
visual.property,
sep = "/"),
base.url = base.url)
node.props <- c(node.props, unlist(unname(res['value'])))
}
node.props <- setNames(node.props, node.names)
return(node.props)
}
}
# ------------------------------------------------------------------------------
#' @title Get Edge Property Values
#'
#' @description Get values for any edge property of the specified edges.
#' @param edge.names List of edge names or SUIDs. Default is NULL for all edges.
#' @param visual.property Name of a visual property. See \link{getVisualPropertyNames}.
#' @param network (optional) Name or SUID of the network. Default is the
#' "current" network active in Cytoscape.
#' @param base.url (optional) Ignore unless you need to specify a custom domain,
#' port or version to connect to the CyREST API. Default is http://localhost:1234
#' and the latest version of the CyREST API supported by this version of RCy3.
#' @details This method retrieves the actual property of the node, given the
#' current visual style, factoring together any default, mapping and bypass setting.
#' @return Named list of property values
#' @examples \donttest{
#' getEdgeProperty(c('node 0 (pp) node 1','node 0 (pp) node 2'),'EDGE_WIDTH')
#' }
#' @export
getEdgeProperty <- function(edge.names = NULL,
visual.property,
network = NULL,
base.url = .defaultBaseUrl) {
net.SUID <- getNetworkSuid(network,base.url)
net.views.SUIDs <- getNetworkViews(net.SUID, base.url)
view.SUID <- as.character(net.views.SUIDs[[1]])
if (is.null(edge.names)){
res <- cyrestGET(paste("networks",
net.SUID,
"views",
view.SUID,
"edges",
sep = "/"),
c(visualProperty=visual.property),
base.url = base.url)
edge.suids <- unlist(lapply(res, function(x) x$SUID))
edge.props <- unlist(lapply(res, function(x) unlist(x$view)['value']))
edge.props <- setNames(edge.props,.edgeSUIDToEdgeName(edge.suids))
return(edge.props)
} else {
edge.SUIDs <-
.edgeNameToEdgeSUID(edge.names, network=net.SUID, base.url=base.url)
edge.props <- c()
for (i in seq_len(length(edge.SUIDs))) {
edge.SUID <- as.character(edge.SUIDs[i])
res <- cyrestGET(paste( "networks",
net.SUID,
"views",
view.SUID,
"edges",
edge.SUID,
visual.property,
sep = "/"),
base.url = base.url)
edge.props <- c(edge.props, unlist(unname(res['value'])))
}
edge.props <- setNames(edge.props, edge.names)
return(edge.props)
}
}
# ------------------------------------------------------------------------------
#' @title Get Network Property Values
#'
#' @description Get values for any network property.
#' @param visual.property Name of a visual property. See \link{getVisualPropertyNames}.
#' @param network (optional) Name or SUID of the network. Default is the "current" network active in Cytoscape.
#' @param base.url (optional) Ignore unless you need to specify a custom domain,
#' port or version to connect to the CyREST API. Default is http://localhost:1234
#' and the latest version of the CyREST API supported by this version of RCy3.
#' @details This method retrieves the actual property of the node, given the
#' current visual style, factoring together any default, mapping and bypass setting.
#' @return Named list of property values
#' @examples \donttest{
#' getNetworkProperty('NETWORK_SCALE_FACTOR')
#' }
#' @export
getNetworkProperty <- function(visual.property,
network = NULL,
base.url = .defaultBaseUrl) {
net.SUID <- getNetworkSuid(network,base.url)
net.views.SUIDs <- getNetworkViews(net.SUID, base.url)
view.SUID <- as.character(net.views.SUIDs[[1]])
res <- cyrestGET(paste("networks",
net.SUID,
"views",
view.SUID,
"network",
visual.property,
sep = "/"),
base.url = base.url)
return(unlist(unname(res['value'])))
}
# ==============================================================================
# II. Specific Functions
# ==============================================================================
# II.a. Node Properties
# Pattern: call getNodeProperty()
# ------------------------------------------------------------------------------
#' @title Get Node Color
#'
#' @description Retrieve the actual fill color of specified nodes.
#' @param node.names List of node names or SUIDs. Default is NULL for all nodes.
#' @param network (optional) Name or SUID of the network. Default is the
#' "current" network active in Cytoscape.
#' @param base.url (optional) Ignore unless you need to specify a custom domain,
#' port or version to connect to the CyREST API. Default is http://localhost:1234
#' and the latest version of the CyREST API supported by this version of RCy3.
#' @return Named list of property values
#' @examples \donttest{
#' getNodeColor()
#' }
#' @export
getNodeColor <- function (node.names=NULL, network=NULL, base.url =.defaultBaseUrl) {
getNodeProperty(node.names, "NODE_FILL_COLOR", network=network, base.url = base.url)
}
# ------------------------------------------------------------------------------
#' @title Get Node Size
#'
#' @description Retrieve the actual size of specified nodes.
#' @param node.names List of node names or SUIDs. Default is NULL for all nodes.
#' @param network (optional) Name or SUID of the network. Default is the
#' "current" network active in Cytoscape.
#' @param base.url (optional) Ignore unless you need to specify a custom domain,
#' port or version to connect to the CyREST API. Default is http://localhost:1234
#' and the latest version of the CyREST API supported by this version of RCy3.
#' @return Named list of property values
#' @examples \donttest{
#' getNodeSize()
#' }
#' @export
getNodeSize <- function (node.names=NULL, network=NULL, base.url =.defaultBaseUrl) {
getNodeProperty(node.names, "NODE_SIZE", network=network, base.url = base.url)
}
# ------------------------------------------------------------------------------
#' @title Get Node Width
#'
#' @description Retrieve the actual width of specified nodes.
#' @param node.names List of node names or SUIDs. Default is NULL for all nodes.
#' @param network (optional) Name or SUID of the network. Default is the
#' "current" network active in Cytoscape.
#' @param base.url (optional) Ignore unless you need to specify a custom domain,
#' port or version to connect to the CyREST API. Default is http://localhost:1234
#' and the latest version of the CyREST API supported by this version of RCy3.
#' @return Named list of property values
#' @examples \donttest{
#' getNodeWidth()
#' }
#' @export
getNodeWidth <- function (node.names=NULL, network=NULL, base.url =.defaultBaseUrl) {
getNodeProperty(node.names, "NODE_WIDTH", network=network, base.url = base.url)
}
# ------------------------------------------------------------------------------
#' @title Get Node Height
#'
#' @description Retrieve the actual height of specified nodes.
#' @param node.names List of node names or SUIDs. Default is NULL for all nodes.
#' @param network (optional) Name or SUID of the network. Default is the
#' "current" network active in Cytoscape.
#' @param base.url (optional) Ignore unless you need to specify a custom domain,
#' port or version to connect to the CyREST API. Default is http://localhost:1234
#' and the latest version of the CyREST API supported by this version of RCy3.
#' @return Named list of property values
#' @examples \donttest{
#' getNodeHeight()
#' }
#' @export
getNodeHeight <- function (node.names=NULL, network=NULL, base.url =.defaultBaseUrl) {
getNodeProperty(node.names, "NODE_HEIGHT", network=network, base.url = base.url)
}
# ------------------------------------------------------------------------------
#' @title Get Node Position
#'
#' @description Retrieve the actual x,y position of specified nodes.
#' @param node.names List of node names or SUIDs. Default is NULL for all nodes.
#' @param network (optional) Name or SUID of the network. Default is the
#' "current" network active in Cytoscape.
#' @param base.url (optional) Ignore unless you need to specify a custom domain,
#' port or version to connect to the CyREST API. Default is http://localhost:1234
#' and the latest version of the CyREST API supported by this version of RCy3.
#' @return Dataframe of x, y values
#' @examples \donttest{
#' getNodePosition()
#' }
#' @export
getNodePosition <- function (node.names=NULL, network=NULL, base.url =.defaultBaseUrl) {
x_location <- getNodeProperty(node.names, "NODE_X_LOCATION", network=network, base.url = base.url)
y_location <- getNodeProperty(node.names, "NODE_Y_LOCATION", network=network, base.url = base.url)
node.pos <- merge(as.data.frame(x_location), as.data.frame(y_location), by = "row.names")
row.names(node.pos) <- node.pos$Row.names
node.pos[,-1]
}
# ==============================================================================
# II.b. Edge Properties
# Pattern: call getEdgeProperty()
# ------------------------------------------------------------------------------
#' @title Get Edge Line Width
#'
#' @description Retrieve the actual line width of specified edges.
#' @param edge.names List of edge names or SUIDs. Default is NULL for all edges.
#' @param network (optional) Name or SUID of the network. Default is the
#' "current" network active in Cytoscape.
#' @param base.url (optional) Ignore unless you need to specify a custom domain,
#' port or version to connect to the CyREST API. Default is http://localhost:1234
#' and the latest version of the CyREST API supported by this version of RCy3.
#' @return Named list of property values
#' @examples \donttest{
#' getEdgeLineWidth()
#' }
#' @export
getEdgeLineWidth <- function (edge.names=NULL, network=NULL, base.url =.defaultBaseUrl) {
getEdgeProperty(edge.names, "EDGE_WIDTH", network=network, base.url = base.url)
}
# ------------------------------------------------------------------------------
#' @title Get Edge Color
#'
#' @description Retrieve the actual line color of specified edges.
#' @param edge.names List of edge names or SUIDs. Default is NULL for all edges.
#' @param network (optional) Name or SUID of the network. Default is the
#' "current" network active in Cytoscape.
#' @param base.url (optional) Ignore unless you need to specify a custom domain,
#' port or version to connect to the CyREST API. Default is http://localhost:1234
#' and the latest version of the CyREST API supported by this version of RCy3.
#' @return Named list of property values
#' @examples \donttest{
#' getEdgeColor()
#' }
#' @export
getEdgeColor <- function (edge.names=NULL, network=NULL, base.url =.defaultBaseUrl) {
getEdgeProperty(edge.names, "EDGE_PAINT", network=network, base.url = base.url)
}
# ------------------------------------------------------------------------------
#' @title Get Edge Line Style
#'
#' @description Retrieve the actual line style of specified edges.
#' @param edge.names List of edge names or SUIDs. Default is NULL for all edges.
#' @param network (optional) Name or SUID of the network. Default is the
#' "current" network active in Cytoscape.
#' @param base.url (optional) Ignore unless you need to specify a custom domain,
#' port or version to connect to the CyREST API. Default is http://localhost:1234
#' and the latest version of the CyREST API supported by this version of RCy3.
#' @return Named list of property values
#' @examples \donttest{
#' getEdgeLineStyle()
#' }
#' @export
getEdgeLineStyle <- function (edge.names=NULL, network=NULL, base.url =.defaultBaseUrl) {
getEdgeProperty(edge.names, "EDGE_LINE_TYPE", network=network, base.url = base.url)
}
# ------------------------------------------------------------------------------
#' @title Get Edge Target Arrow Shape
#'
#' @description Retrieve the actual target arrow shape of specified edges.
#' @param edge.names List of edge names or SUIDs. Default is NULL for all edges.
#' @param network (optional) Name or SUID of the network. Default is the
#' "current" network active in Cytoscape.
#' @param base.url (optional) Ignore unless you need to specify a custom domain,
#' port or version to connect to the CyREST API. Default is http://localhost:1234
#' and the latest version of the CyREST API supported by this version of RCy3.
#' @return Named list of property values
#' @examples \donttest{
#' getEdgeTargetArrowShape()
#' }
#' @export
getEdgeTargetArrowShape <- function (edge.names=NULL, network=NULL, base.url =.defaultBaseUrl) {
getEdgeProperty(edge.names, "EDGE_TARGET_ARROW_SHAPE", network=network, base.url = base.url)
}
# ==============================================================================
# II.c. Network Properties
# Pattern: call getNetworkProperty()
# ------------------------------------------------------------------------------
#' @title Get Network Center
#'
#' @description Retrieve the center of specified network.
#' @param network (optional) Name or SUID of the network. Default is the
#' "current" network active in Cytoscape.
#' @param base.url (optional) Ignore unless you need to specify a custom domain,
#' port or version to connect to the CyREST API. Default is http://localhost:1234
#' and the latest version of the CyREST API supported by this version of RCy3.
#' @return Named list of property values
#' @examples \donttest{
#' getNetworkCenter()
#' }
#' @export
getNetworkCenter <- function(network=NULL, base.url =.defaultBaseUrl) {
x.coordinate <- getNetworkProperty("NETWORK_CENTER_X_LOCATION",
network = network, base.url = base.url)
y.coordinate <- getNetworkProperty("NETWORK_CENTER_Y_LOCATION",
network = network, base.url = base.url)
return(list(x = x.coordinate, y = y.coordinate))
}
# ------------------------------------------------------------------------------
#' @title Get Network Zoom
#'
#' @description Retrieve the scale factor of specified network.
#' @param network (optional) Name or SUID of the network. Default is the
#' "current" network active in Cytoscape.
#' @param base.url (optional) Ignore unless you need to specify a custom domain,
#' port or version to connect to the CyREST API. Default is http://localhost:1234
#' and the latest version of the CyREST API supported by this version of RCy3.
#' @return Named list of property values
#' @examples \donttest{
#' getNetworkZoom()
#' }
#' @export
getNetworkZoom <- function(network=NULL, base.url =.defaultBaseUrl) {
getNetworkProperty("NETWORK_SCALE_FACTOR", network = network, base.url = base.url)
}
