R/edges.r

In rggobi: Interface Between R and 'GGobi'

# Get edges
# Get edges for a dataset
#
# @arguments ggobi dataset
# @value A matrix of edge pairs
# @keyword manip
edges <- function(x) {
	m <- .GGobiCall("getSymbolicEdges", x)
	if (ncol(m) == 2) colnames(m) <- c("source", "destination")
	m
}

# Get connecting edges
# Get actual edges from application of edges dataset to target dataset.
#
# @arguments target ggobi dataset
# @arguments ggobi dataset containing edges
# @keyword manip
connecting_edges <- function(x, y) {
	m <- .GGobiCall("getConnectedEdges", y, x) + 1
	if (ncol(m) == 2) colnames(m) <- c("source", "destination")
	m
}

# Set edges
# Generic method, see methods for more details
#
# @keyword internal
"edges<-" <- function(x, value) UseMethod("edges<-", x)


# Set edges
# Set edges for a dataset.
#
# In GGobi, and edge dataset is a special type of dataset that has
# two additional (hidden) columns which specification source and
# destination row names.  These rownames are compared to the row
# names of the dataset in the current plot, and if any match, it
# is possible to specify this dataset as an edge set to the plotted
# datset.  When this is done, edges will be drawn between points
# specified by the edge dataset.
#
# To remove edges, set edges to NULL.
#
# @arguments GGobiData
# @arguments matrix, data frame, or graph containing of edges.  First column should be from edge, second column to edge.
# @keyword manip
# @seealso \code{\link{ggobi_longitudinal}} for creating edges which simulate time series plots
#X cc<-cor(t(swiss),use="p", method="s")
#X ccd<-sqrt(2*(1-cc))
#X a <- which(lower.tri(ccd), arr.ind=TRUE)
#X src <- row.names(swiss)[a[,2]]
#X dest <- row.names(swiss)[a[,1]]
#X weight <- as.vector(as.dist(ccd))
#X gg <- ggobi(swiss)
#X gg$cor <- data.frame(weight)
#X edges(gg$cor) <- cbind(src, dest)
#X edges(gg$cor)
#X edges(gg$cor) <- NULL
"edges<-.GGobiData" <- function(x, value) {
  if (is.null(value)) return(invisible(.GGobiCall("setEdges", character(0), character(0), FALSE, x)))

#   if(is(value, "graphNEL")) {
#     value <- matrix(graph::nodes(value)[t(graph::edgeMatrix(value))], ncol=2)
#   }

  src  <- value[,1]
  dest <- value[,2]


	if (is.numeric(src)) src <- rownames(x)[src]
	if (is.numeric(dest)) dest <- rownames(x)[dest]

	.GGobiCall("setEdges", as.character(src), as.character(dest), FALSE, x)
	x
}


# Set edges
# Set edges for a display
#
# This sets the dataset that a GGobiDisplay uses
# to display edges.
#
# @arguments GGobiDisplay object
# @arguments GGobiData object that contains edges
# @keyword dynamic
"edges<-.GGobiDisplay" <- function(x, value) {
	if (is.null(value)) {
		.GGobiCall("setDisplayEdges", list(x), value, FALSE, FALSE)
	} else {
		.GGobiCall("setDisplayEdges", list(x), value, FALSE, TRUE)
	}
	x
}

# Set edges
# Create a new edges dataset and add to GGobi
#
# @arguments GGobi dataset
# @arguments new edges
#
# @keyword dynamic
"edges<-.GGobi" <- function(x, value) {
  name <- deparse(substitute(value))
#   if(is(value, "graphNEL")) {
#     names <- graph::nodes(value)
#     value <- t(graph::edgeMatrix(value))
#     value <- cbind(names[value[, 1]], names[value[, 2]])
#   }
  df <- data.frame(id=1:nrow(value))
  rownames(df) <- paste(name, 1:nrow(df), sep="")
  x[[name]] <- df
  y <- x[[name]]
  edges(y) <- value

  x
}