R/network.R
In mixOmicsTeam/mixOmics: Omics Data Integration Project
Defines functions
network
Documented in
network
#' Relevance Network for (r)CCA and (s)PLS regression
#'
#' Display relevance associations network for (regularized) canonical
#' correlation analysis and (sparse) PLS regression. The function avoids the
#' intensive computation of Pearson correlation matrices on large data set by
#' calculating instead a pair-wise similarity matrix directly obtained from the
#' latent components of our integrative approaches (CCA, PLS, block.pls
#' methods). The similarity value between a pair of variables is obtained by
#' calculating the sum of the correlations between the original variables and
#' each of the latent components of the model. The values in the similarity
#' matrix can be seen as a robust approximation of the Pearson correlation (see
#' González et al. 2012 for a mathematical demonstration and exact formula).
#' The advantage of relevance networks is their ability to simultaneously
#' represent positive and negative correlations, which are missed by methods
#' based on Euclidean distances or mutual information. Those networks are
#' bipartite and thus only a link between two variables of different types can
#' be represented. The network can be saved in a .glm format using the
#' \code{igraph} package, the function \code{write.graph} and extracting the
#' output \code{object$gR}, see details.
#'
#' \code{network} allows to infer large-scale association networks between the
#' \eqn{X} and \eqn{Y} datasets in \code{rcc} or \code{spls}. The output is a
#' graph where each \eqn{X}- and \eqn{Y}-variable corresponds to a node and the
#' edges included in the graph portray associations between them.
#'
#' In \code{rcc}, to identify \eqn{X}-\eqn{Y} pairs showing relevant
#' associations, \code{network} calculate a similarity measure between \eqn{X}
#' and \eqn{Y} variables in a pair-wise manner: the scalar product value
#' between every pairs of vectors in dimension \code{length(comp)} representing
#' the variables \eqn{X} and \eqn{Y} on the axis defined by \eqn{Z_i} with
#' \eqn{i} in \code{comp}, where \eqn{Z_i} is the equiangular vector between
#' the \eqn{i}-th \eqn{X} and \eqn{Y} canonical variate.
#'
#' In \code{spls}, if \code{object$mode} is \code{regression}, the similarity
#' measure between \eqn{X} and \eqn{Y} variables is given by the scalar product
#' value between every pairs of vectors in dimension \code{length(comp)}
#' representing the variables \eqn{X} and \eqn{Y} on the axis defined by
#' \eqn{U_i} with \eqn{i} in \code{comp}, where \eqn{U_i} is the \eqn{i}-th
#' \eqn{X} variate. If \code{object$mode} is \code{canonical} then \eqn{X} and
#' \eqn{Y} are represented on the axis defined by \eqn{U_i} and \eqn{V_i}
#' respectively.
#'
#' Variable pairs with a high similarity measure (in absolute value) are
#' considered as relevant. By changing the cut-off, one can tune the relevance
#' of the associations to include or exclude relationships in the network.
#'
#' \code{interactive=TRUE} open two device, one for association network, one
#' for scrollbar, and define an interactive process: by clicking either at each
#' end (\eqn{-} or \eqn{+}) of the scrollbar or at middle portion of this.
#' The position of the slider indicate which is the `cutoff' value associated
#' to the display network.
#'
#' The network can be saved in a .glm format using the \pkg{igraph} package,
#' the function \code{write.graph} and extracting the output \code{obkect$gR}.
#'
#' The interactive process is terminated by clicking the second button and
#' selecting \code{Stop} from the menu, or from the \code{Stop} menu on the graphics
#' window.
#'
#' The \code{color.node} is a vector of length two, of any of the three kind of
#' \code{R} colors, i.e., either a color name (an element of \code{colors()}),
#' a hexadecimal string of the form \code{"#rrggbb"}, or an integer \code{i}
#' meaning \code{palette()[i]}. \code{color.node[1]} and \code{color.node[2]}
#' give the color for filled nodes of the \eqn{X}- and \eqn{Y}-variables
#' respectively. Defaults to \code{c("white", "white")}.
#'
#' \code{color.edge} give the color to edges with colors corresponding to the
#' values in \code{mat}. Defaults to \code{color.GreenRed(100)} for negative
#' (green) and positive (red) correlations. We also propose other palettes of
#' colors, such as \code{color.jet} and \code{color.spectral}, see help on
#' those functions, and examples below. Other palette of colors from the stats
#' package can be used too.
#'
#' \code{shape.node[1]} and \code{shape.node[2]} provide the shape of the nodes
#' associate to \eqn{X}- and \eqn{Y}-variables respectively. Current acceptable
#' values are \code{"circle"} and \code{"rectangle"}. Defaults to
#' \code{c("circle", "rectangle")}.
#'
#' \code{lty.edge[1]} and \code{lty.egde[2]} give the line type to edges with
#' positive and negative weight respectively. Can be one of \code{"solid"},
#' \code{"dashed"}, \code{"dotted"}, \code{"dotdash"}, \code{"longdash"} and
#' \code{"twodash"}. Defaults to \code{c("solid", "solid")}.
#'
#' \code{lwd.edge[1]} and \code{lwd.edge[2]} provide the line width to edges
#' with positive and negative weight respectively. This attribute is of type
#' double with a default of \code{c(1, 1)}.
#'
#' @aliases network network.default network.rcc network.pls network.spls
#' @param mat numeric matrix of values to be represented. Alternatively,
#' an object from one of the following models: \code{mix_pls}, \code{plsda},
#' \code{mixo_spls}, \code{splsda}, \code{rcc}, \code{sgcca}, \code{rgcca},
#' \code{sgccda}.
#' @param comp atomic or vector of positive integers. The components to
#' adequately account for the data association. Defaults to \code{comp = 1}.
#' @param cutoff numeric value between \code{0} and \code{1}. The tuning
#' threshold for the relevant associations network (see Details).
#' @param row.names,col.names character vector containing the names of \eqn{X}-
#' and \eqn{Y}-variables.
#' @param graph.scale Numeric between 0 and 1 which alters the scale of the entire
#' plot. Increasing the value decreases the size of nodes and increases their distance
#' from one another. Defaults to 0.5.
#' @param size.node Numeric between 0 and 1 which determines the relative size of nodes.
#' Defaults to 0.5.
#' @param color.node vector of length two, the colors of the \eqn{X} and
#' \eqn{Y} nodes (see Details).
#' @param shape.node character vector of length two, the shape of the \eqn{X}
#' and \eqn{Y} nodes (see Details).
#' @param alpha.node Numeric between 0 and 1 which determines the opacity of nodes.
#' Only used in block objects.
#' @param color.edge vector of colors or character string specifying the colors
#' function to using to color the edges, set to default to
#' \code{color.GreenRed(100)} but other palettes can be chosen (see Details and
#' Examples).
#' @param lty.edge character vector of length two, the line type for the edges
#' (see Details).
#' @param lwd.edge vector of length two, the line width of the edges (see
#' Details).
#' @param show.edge.labels logical. If \code{TRUE}, plot association values as
#' edge labels (defaults to \code{FALSE}).
#' @param show.color.key Logical. If \code{TRUE} a color key should be plotted.
#' @param symkey Logical indicating whether the color key should be made
#' symmetric about 0. Defaults to \code{TRUE}.
#' @param keysize numeric value indicating the size of the color key.
#' @param keysize.label vector of length 1, indicating the size of the labels
#' and title of the color key.
#' @param breaks (optional) either a numeric vector indicating the splitting
#' points for binning \code{mat} into colors, or a integer number of break
#' points to be used, in which case the break points will be spaced equally
#' between \code{min(mat)} and \code{max(mat)}.
#' @param interactive logical. If \code{TRUE}, a scrollbar is created to change
#' the cutoff value interactively (defaults to \code{FALSE}). See Details.
#' @param save should the plot be saved ? If so, argument to be set either to
#' \code{'jpeg'}, \code{'tiff'}, \code{'png'} or \code{'pdf'}.
#' @param name.save character string giving the name of the saved file.
#' @param cex.edge.label the font size for the edge labels.
#' @param cex.node.name the font size for the node labels.
#' @param blocks a vector indicating the block variables to display.
#' @param block.var.names either a list of vector components for variable names
#' in each block or FALSE for no names. If TRUE, the columns names of the
#' blocks are used as names.
#' @param layout.fun a function. It specifies how the vertices will be placed
#' on the graph. See help(layout) in the igraph package. Defaults to
#' layout.fruchterman.reingold.
#' @param plot.graph logical. If \code{TRUE} (default), plotting window will be
#' filled with network. If \code{FALSE}, then no graph will be plotted, though
#' the return value of the function is the exact same.
#' @return \code{network} return a list containing the following components:
#' \item{M}{the correlation matrix used by \code{network}.} \item{gR}{a
#' \code{graph} object to save the graph for cytoscape use (requires to load
#' the \pkg{igraph} package).}
#' @section Warning: If the number of variables is high, the generation of the
#' network generation can take some time.
#' @author Ignacio González, Kim-Anh Lê Cao, AL J Abadi
#' @seealso \code{\link{plotVar}}, \code{\link{cim}},
#' \code{\link{color.GreenRed}}, \code{\link{color.jet}},
#' \code{\link{color.spectral}} and http: //www.mixOmics.org for more details.
#' @references Mathematical definition: González I., Lê Cao K-A., Davis, M.J.
#' and Déjean, S. (2012). Visualising associations between paired omics data
#' sets. J. Data Mining 5:19.
#' \url{http://www.biodatamining.org/content/5/1/19/abstract}
#'
#' Examples and illustrations:
#'
#' Rohart F, Gautier B, Singh A, Lê Cao K-A. mixOmics: an R package for 'omics
#' feature selection and multiple data integration. PLoS Comput Biol 13(11):
#' e1005752
#'
#' Relevance networks:
#'
#' Butte, A. J., Tamayo, P., Slonim, D., Golub, T. R. and Kohane, I. S. (2000).
#' Discovering functional relationships between RNA expression and
#' chemotherapeutic susceptibility using relevance networks. \emph{Proceedings
#' of the National Academy of Sciences of the USA} \bold{97}, 12182-12186.
#'
#' Moriyama, M., Hoshida, Y., Otsuka, M., Nishimura, S., Kato, N., Goto, T.,
#' Taniguchi, H., Shiratori, Y., Seki, N. and Omata, M. (2003). Relevance
#' Network between Chemosensitivity and Transcriptome in Human Hepatoma Cells.
#' \emph{Molecular Cancer Therapeutics} \bold{2}, 199-205.
#' @keywords multivariate graphs dplot hplot iplot
#' @export
#' @example ./examples/network-examples.R
network <- function(mat,
comp = NULL,
blocks = c(1, 2),
cutoff = 0,
row.names = TRUE,
col.names = TRUE,
block.var.names = TRUE,
graph.scale = 0.5,
size.node = 0.5,
color.node = NULL,
shape.node = NULL,
alpha.node = 0.85,
cex.node.name = NULL,
color.edge = color.GreenRed(100),
lty.edge = "solid",
lwd.edge = 1,
show.edge.labels = FALSE,
cex.edge.label = 1,
show.color.key = TRUE,
symkey = TRUE,
keysize = c(1, 1),
keysize.label = 1,
breaks,
interactive = FALSE,
layout.fun = NULL,
save = NULL,
name.save = NULL,
plot.graph = TRUE
)
{
#-- checking general input parameters --------------------------------------#
#---------------------------------------------------------------------------#
#-- check that the user did not enter extra arguments
arg.call = match.call()
user.arg = names(arg.call)[-1]
err = tryCatch(mget(names(formals()), sys.frame(sys.nframe())),
error = function(e) e)
if ("simpleError" %in% class(err))
stop(err[[1]], ".", call. = FALSE)
function.arg = names(mget(names(formals()), sys.frame(sys.nframe())))
not.arg = !(user.arg %in% function.arg)
if (any(not.arg))
{
unused.arg = user.arg[not.arg]
not.arg = which(not.arg) + 1
output = rep("", length(not.arg))
for (i in 1:length(not.arg))
{
output[i] = paste0(unused.arg[i], " = ", arg.call[[not.arg[i]]])
}
output = paste0("(", paste(output, collapse = ", "), ").")
msg = "unused argument "
if (length(not.arg) > 1) msg = "unused arguments "
stop(msg, output, call. = FALSE)
}
# #-- check blocks
# if(length(blocks) != 2)
# stop("We can only display 2 blocks",call.=FALSE)
#-- save
if (!is.null(save))
{
if (! save %in% c("jpeg","tiff","png","pdf"))
stop("'save' must be one of 'jpeg', 'png', 'tiff' or 'pdf'.", call. = FALSE)
}
#-- name.save
if (!is.null(name.save))
{
if (! is.character(name.save) || length(name.save) > 1)
stop("'name.save' must be a character.", call. = FALSE)
} else {
if (!is.null(save))
name.save = paste0("network_",gsub(".", "_", deparse(substitute(mat)) ,fixed = TRUE))
}
if (!is.null(save)){
while (dev.cur()>1)
dev.off()
if (save == "jpeg")
jpeg(filename = paste0(name.save,".jpeg"), res = 600, width = 4000, height = 4000)
if (save == "png")
jpeg(filename = paste0(name.save,".png"), res = 600, width = 4000, height = 4000)
if (save == "tiff")
tiff(filename = paste0(name.save,".tiff"), res = 600, width = 4000, height = 4000)
if (save == "pdf")
pdf(file = paste0(name.save,".pdf"))
}
if (!plot.graph & interactive) {
stop("plot.graph cannot be FALSE if interactive = TRUE", call.=FALSE)
}
class.object = class(mat)
object.pls=c("mixo_pls","mixo_spls","mixo_mlspls")
object.rcc="rcc"
object.blocks=c("sgcca","rgcca")
if (! any(class.object %in% c(object.pls,object.rcc,object.blocks, "matrix")))
stop( " 'network' is only implemented for the following objects: matrix, pls, plsda, spls, splsda, rcc, sgcca, rgcca, sgccda", call.=FALSE)
if(any(class.object %in% c(object.rcc,object.pls)))
{
p = ncol(mat$X)
if(any(class.object == "DA")) # object is DA
mat$Y = mat$ind.mat
q = ncol(mat$Y)
n = nrow(mat$X)
ncomp = mat$ncomp
#-- comp
if(is.null(comp))
comp=1:mat$ncomp
if (length(comp) == 1)
{
if(comp>ncomp)
{
stop("the elements of 'comp' must be smaller than or equal to ", ncomp, ".",
call. = FALSE)
} else if ( !is.numeric(comp) || comp <= 0) {
stop("invalid value for 'comp'.", call. = FALSE)
}
}
if (length(comp) > 1)
{
if(length(comp) > ncomp)
stop("the length of 'comp' must be smaller than or equal to ", ncomp, ".",
call. = FALSE)
if (!is.numeric(comp) || any(comp < 1))
stop("invalid vector for 'comp'.", call. = FALSE)
if (any(comp > ncomp))
stop("the elements of 'comp' must be <= ", ncomp, ".",
call. = FALSE)
}
comp = round(comp)
#-- row.names
row.names.plot = TRUE # whether to plot the label in the graph
if (is.logical(row.names))
{
if(!isTRUE(row.names))
{
row.names.plot = FALSE
}
row.names = mat$names$colnames$X
} else {
row.names = as.vector(row.names)
if (length(unique(row.names)) != p)
stop("'row.names' must be a character vector of ", p, " unique entries.",
call. = FALSE)
}
if(row.names.plot == TRUE)
{
row.names.plot = row.names
}else{
row.names.plot = rep("",p)
}
#-- col.names
col.names.plot = TRUE # whether to plot the label in the graph
if (is.logical(col.names))
{
if(!isTRUE(col.names))
{
col.names.plot = FALSE
}
col.names = mat$names$colnames$Y
} else {
col.names = as.vector(col.names)
if (length(col.names) != q)
stop("'col.names' must be a character vector of ", q, " unique entries.",
call. = FALSE)
}
if(col.names.plot == TRUE)
{
col.names.plot = col.names
}else{
col.names.plot = rep("",q)
}
#-- end checking --#
#------------------#
#-- network ----------------------------------------------------------------#
#---------------------------------------------------------------------------#
if(any(class.object %in% object.rcc))
{
#-- similarity matrix --#
bisect = mat$variates$X[, comp] + mat$variates$Y[, comp]
cord.X = cor(mat$X, bisect, use = "pairwise")
cord.Y = cor(mat$Y, bisect, use = "pairwise")
mat = cord.X %*% t(cord.Y)
} else if(any(class.object %in% object.pls)) {
#-- variable selection --#
if (all(class(mat) %in% "mixo_pls"))
{
keep.X = rep(TRUE,p)
keep.Y = rep(TRUE,q)
} else {
keep.X = apply(abs(mat$loadings$X[, comp, drop=FALSE]), 1, sum) > 0
keep.Y = apply(abs(mat$loadings$Y[, comp, drop=FALSE]), 1, sum) > 0
row.names = row.names[keep.X]
col.names = col.names[keep.Y]
}
#-- similarity matrix --#
if (mat$mode == "canonical")
{
cord.X = cor(mat$X[, keep.X], mat$variates$X[, comp], use = "pairwise")
cord.Y = cor(mat$Y[, keep.Y], mat$variates$Y[, comp], use = "pairwise")
} else {
cord.X = cor(mat$X[, keep.X], mat$variates$X[, comp], use = "pairwise")
cord.Y = cor(mat$Y[, keep.Y], mat$variates$X[, comp], use = "pairwise")
}
mat = cord.X %*% t(cord.Y)
}
} else if(any(class.object %in% object.blocks)) {
mat$X <- mapply(mat$X, names(mat$X), FUN = function(x, y)
{
colnames(x) <- paste0(colnames(x),"_", y)
x
}, SIMPLIFY = FALSE)
# remove Y from the list of blocks for DA objects
if(any(class.object == "DA"))
{
mat$names$blocks = mat$names$blocks [-mat$indY]
mat$names$colnames = mat$names$colnames [-mat$indY]
mat$ncomp = mat$ncomp [-mat$indY]
}
if (is.null(blocks))
{
if (any(mat$ncomp > 1))
{
blocks = mat$names$blocks[ which(mat$ncomp > 1)]
} else {
stop(("The number of components for each block is 1. The number of components must be superior or equal to 2."), call. = FALSE)
}
} else if (is.numeric(blocks) & min(blocks) > 0 & max(blocks) <= length(mat$names$blocks)) {
blocks = mat$names$blocks[blocks]
} else if (is.character(blocks)) {
if (!all(blocks %in% mat$names$blocks))
stop("One element of 'blocks' does not match with the names of the blocks")
} else {
stop("Incorrect value for 'blocks", call. = FALSE)
}
#-- comp
if (is.null(comp))
{
comp = vector("list", length(blocks))
names(comp) = blocks
for (i in blocks)
comp[[i]] = 1:mat$ncomp[i]
}
if (is.list(comp))
{
if (length(comp) != length(blocks))
stop("'comp' must be either NULL a list of length ", length(blocks), ".",
call. = FALSE)
if (!all(blocks %in% names(comp)))
stop("names of 'comp' must be from {",
paste(blocks, collapse = ", "), "}.", call. = FALSE)
for (i in blocks)
{
if (any(!is.finite(comp[[i]])))
stop("invalid value for 'comp' of the block '", i, "'.", call. = FALSE)
if (any(comp[[i]] > mat$ncomp[i]))
stop("the elements of 'comp' for block '", i, "' must be <= ",
mat$ncomp[i], ".", call. = FALSE)
if (any(comp[[i]] < 1))
stop("invalid value for 'comp' of the block '", i, "'.", call. = FALSE)
}
} else {
stop("'comp' must be either NULL or a list of length ", length(blocks), ".",
call. = FALSE)
}
#-- block.var.names
num.var = unlist(lapply(mat$X[blocks], ncol))
if (is.logical(block.var.names))
{
if (length(block.var.names)==1)
block.var.names=rep(block.var.names,length(blocks))
if (length(block.var.names) != length(blocks))
stop("'block.var.names' must be a logical vector of length 1 or ", length(blocks),", or a list of length ", length(blocks), ".",
call. = FALSE)
vec=(which(block.var.names==FALSE))
block.var.names = mat$names$colnames
for (i in 1:length(blocks))
{
if (i %in% vec)
block.var.names[[blocks[i]]] = rep(" ",length(mat$names$colnames[[blocks[i]]]))
}
} else {
if (is.list(block.var.names))
{
if (length(block.var.names) != length(blocks))
{
stop("'block.var.names' must be a logical vector or a list of length ", length(blocks), ".",
call. = FALSE)
} else {
if (!all(unlist(lapply(block.var.names, is.vector))))
stop("each component of 'block.var.names' must be a vector.", call. = FALSE)
block.var.names.length = unlist(lapply(block.var.names, length))
if (any(block.var.names.length != num.var))
stop("components of 'block.var.names' must be vectors of length ",
paste(num.var, collapse = ", "), ".", call. = FALSE)
}
} else {
stop("'block.var.names' must be either a logical value or a list of length ",
length(blocks), ".", call. = FALSE)
}
}
#-- network approach -------------------------------------------------------#
#---------------------------------------------------------------------------#
#-- calculation of the similarity matrix for each block --#
coord = M_block = list()
j = 1
if (is(mat, "sgcca"))
{
for (k in blocks)
{
if (length(comp[[k]]) > 1)
{
keep = (apply(abs(mat$loadings[[k]][, comp[[k]]]), 1, sum) > 0)
} else {
keep = abs(mat$loadings[[k]][, comp[[k]]]) > 0
}
coord[[j]] = cor(mat$X[[k]][, keep], mat$variates[[k]][, comp[[k]]], use = "pairwise")
j = j + 1
}
} else {
for(k in blocks)
{
coord[[j]] = cor(mat$X[[k]], mat$variates[[k]][, comp[[k]]], use = "pairwise")
j = j + 1
}
}
node.X = node.Y = w = NULL
l = 1
for (j in 1:(length(blocks) - 1))
{
for (k in (j + 1):length(blocks))
{
if(!any(comp[[blocks[j]]] %in% comp[[blocks[k]]]))
stop("comp of block ",blocks[j], " is ", comp[[blocks[j]]], " but comp of block ", blocks[k]," is ",comp[[blocks[k]]],
call. = FALSE)
int.comp = intersect(comp[[blocks[j]]], comp[[blocks[k]]])
object = coord[[j]][, comp[[blocks[j]]] %in% int.comp] %*% t(coord[[k]][, comp[[blocks[k]]] %in% int.comp])
M_block[[l]] = object
l = l + 1
X = rownames(coord[[j]])
Y = rownames(coord[[k]])
rep.X = rep(X, each = length(Y))
rep.Y = rep(Y, length(X))
node.X = c(node.X, rep.X)
node.Y = c(node.Y, rep.Y)
w = c(w, as.vector(t(object)))
}
}
} else {
#-- mat
if (!is.matrix(mat))
stop("'mat' must be a numeric matrix.", call. = FALSE)
if (length(dim(mat)) != 2)
stop("'mat' must be a numeric matrix.")
if (!is.numeric(mat))
stop("'mat' must be a numeric matrix.")
p = nrow(mat)
q = ncol(mat)
#-- row.names
row.names.plot = TRUE # whether to plot the label in the graph
if (is.logical(row.names))
{
if(!isTRUE(row.names))
{
row.names.plot = FALSE
}
row.names = rownames(mat)
} else {
row.names = as.vector(row.names)
if (length(row.names) != p)
stop("'row.names' must be a character vector of ", p, " unique entries.",
call. = FALSE)
}
if(row.names.plot == TRUE)
{
row.names.plot = row.names
}else{
row.names.plot = rep("",p)
}
#-- col.names
col.names.plot = TRUE # whether to plot the label in the graph
if (is.logical(col.names))
{
if(!isTRUE(col.names))
{
col.names.plot = FALSE
}
col.names = colnames(mat)
} else {
col.names = as.vector(col.names)
if (length(col.names) != q)
stop("'col.names' must be a character vector of ", q, " unique entries.",
call. = FALSE)
}
if(col.names.plot == TRUE)
{
col.names.plot = col.names
}else{
col.names.plot = rep("",q)
}
}
#-- size.node
if (!is.null(size.node)) {
if (!is.finite(size.node) || size.node < 0 || size.node > 1) {
stop("'size.node' must be a numerical value between 0 - 1.", call. = FALSE)
}
if (size.node == 0) {
shape.node <- "none"
size.node <- 1 # prevents error
}
}
#-- graph.scale
if (!is.finite(graph.scale) || graph.scale < 0 || graph.scale > 1) {
stop("'graph.scale' must be a numerical value between 0 - 1.", call. = FALSE)
}
#-- color.node
if(any(class.object %in% object.blocks))
{
if (is.null(color.node))
{
## see circosPlot
color.blocks = brewer.pal(n = 12, name = 'Paired') #why 12?? ANS: bc max allowed n is 12 for this function
if (length(blocks) > 6) {
color.blocks <- colorRampPalette(color.blocks)(2*length(object$X))
}
color.node = color.blocks[seq(from = 1, to = 2*length(blocks), by = 2)]
color.node = adjustcolor(color.node, alpha.f = alpha.node)
names(color.node) = blocks
} else {
if (!is.vector(color.node) || length(color.node) != length(blocks))
stop("'color.node' must be a vector of length ", length(blocks), ".", call. = FALSE)
}
} else {
if(is.null(color.node))
color.node = brewer.pal(n = 12, name = 'Paired')[c(1,3)]
color.node = adjustcolor(color.node, alpha.f = alpha.node)
if (!is.list(color.node))
{
if (!is.vector(color.node) || length(color.node) != 2)
stop("'color.node' must be a vector of length 2.", call. = FALSE)
} else {
stop("'color.node' must be a vector of length 2.", call. = FALSE)
}
}
if (any(!sapply(color.node, function(x){tryCatch(is.matrix(col2rgb(x)), error = function(e) FALSE) })))
stop("'color.node' must be a character vector of recognized colors.",
call. = FALSE)
#-- shape.node
if(any(class.object%in% object.blocks))
{
if (is.null(shape.node))
shape.node = "circle"
if (is.vector(shape.node))
{
if (length(shape.node) == 1)
shape.node = rep(shape.node, length(blocks))
}
if (!is.list(shape.node))
{
if (!is.vector(shape.node) || length(shape.node) != length(blocks))
stop("'shape.node' must be a character vector of length ", length(blocks), ".",
call. = FALSE)
} else {
stop("'shape.node' must be a numeric vector of length ", length(blocks), ".",
call. = FALSE)
}
if (!all(shape.node %in% c("none", "circle", "rectangle")))
stop("elements of 'shape.node' must be from {'none', 'circle', 'rectangle'}.",
call. = FALSE)
if (is.null(names(shape.node)))
names(shape.node) = blocks
} else {
if(is.null(shape.node))
shape.node=c("circle", "rectangle")
if (length(shape.node)==1) {
if(shape.node=="none") {
shape.node=c("none", "none")
}
}
if (!is.list(shape.node))
{
if (!is.vector(shape.node) || length(shape.node) != 2)
stop("'shape.node' must be a vector of length 2.", call. = FALSE)
} else {
stop("'shape.node' must be a vector of length 2.", call. = FALSE)
}
if (!all(shape.node %in% c("none", "circle", "rectangle")))
stop("elements of 'shape.node' must be from {'none', 'circle', 'rectangle'}.",
call. = FALSE)
}
#-- cex.node.name
if (!is.null(cex.node.name)) {
if (!is.finite(cex.node.name) || cex.node.name < 0 || length(cex.node.name)>1) {
stop("'cex.node.name' must be a non-negative numerical value.", call. = FALSE)
}
}
#-- color.edge
if (length(color.edge) < 2 && (!is(color.edge, "function")))
stop("'color.edge' must be a vector of length larger than or equal to 2.", call. = FALSE)
if ((length(color.edge) %% 2) != 0 && (!is(color.edge, "function")) && isTRUE(symkey))
stop("'color.edge' must be a vector of length an even number if 'symkey = TRUE'.", call. = FALSE)
if (any(!sapply(color.edge, function(x) {tryCatch(is.matrix(col2rgb(x)), error = function(e) FALSE) })))
stop("'color.edge' must be a character vector of recognized colors.", call. = FALSE)
#-- lty.edge
if(length(lty.edge) >2)
stop("\"lty.edge\" must a character vector of up to 2 entries from
'solid', 'dashed', 'dotted', 'dotdash', 'longdash', twodash' or 'blank'.
see ?network",
call.=FALSE)
if (length(lty.edge)==1) lty.edge = c(lty.edge, lty.edge)
choices = c("solid", "dashed", "dotted", "dotdash", "longdash", "twodash", "blank")
lty.edge = choices[pmatch(lty.edge, choices,duplicates.ok=TRUE)]
if (any(is.na(lty.edge)))
stop("'lty.edge' should be from 'solid', 'dashed', 'dotted', 'dotdash', 'longdash', twodash' or 'blank'.",
call. = FALSE)
#-- lwd.edge
if(length(lwd.edge) >2)
stop("'lwd.edge' must be a vector of up to 2 positive numbers.
See ?network")
if (length(lwd.edge)==1)
lwd.edge = c(lwd.edge, lwd.edge)
if (length(lwd.edge) != 2 || any(!is.finite(lwd.edge)) || any(lwd.edge <= 0))
stop("'lwd.edge' must be positive.")
#-- show.edge.labels
if (!is.logical(show.edge.labels))
stop("'show.edge.labels' must be a logical constant (TRUE or FALSE).",
call. = FALSE)
#-- cex.edge.label
if (!is.finite(cex.edge.label) || cex.edge.label < 0 || length(cex.edge.label)>1)
stop("'cex.edge.label' must be a non-negative numerical value.", call. = FALSE)
#-- show.color.key
if (!is.logical(show.color.key))
stop("'show.color.key' must be a logical constant (TRUE or FALSE).",
call. = FALSE)
#-- symkey
if (!is.logical(symkey))
stop("'symkey' must be a logical constant (TRUE or FALSE).",
call. = FALSE)
#-- keysize
if (length(keysize) != 2 || any(!is.finite(keysize)))
stop("'keysize' must be a numeric vector of length 2.",
call. = FALSE)
#-- keysize.label
if (length(keysize.label) != 1 || any(!is.finite(keysize)))
stop("'keysize' must be a numeric vector of length 1.",
call. = FALSE)
#-- interactive
if (!is.logical(interactive))
stop("'interactive' must be a logical constant (TRUE or FALSE).",
call. = FALSE)
#-- layout.fun
if (!is.null(layout.fun) && !is(layout.fun, "function"))
stop("'layout.fun' must be a valid layout function.", call. = FALSE)
#-- end checking --#
#------------------#
#-- network approach -------------------------------------------------------#
#---------------------------------------------------------------------------#
if (!(any(class.object %in% object.blocks)))
w = as.vector(t(mat))
#-- check cutoff
if (round(max(abs(w)), 2) == 0)
stop("There is no correlation between these blocks whith these components.",
"Try a different value of 'comp'.", call. = FALSE)
if (!is.numeric(cutoff) || cutoff < 0 || cutoff > 1)
stop("'cutoff' should be a numeric between 0 and 1", call. = FALSE)
if(cutoff > max(abs(w)))
stop("You have chosen a high cutoff value of ", cutoff,
" which is greaer than the max value in the similarity matrix which is ",
round(max(abs(w)), 2), call. = FALSE)
# Definition of nodes #
#---------------------#
#save(list=ls(),file="temp.Rdata")
if(any(class.object %in% object.blocks))
{
group = NULL
temp = lapply(mat$X, function(x) colnames(x))
for (i in 1:length(temp))
{
group = c(group, rep(names(temp)[i], length(temp[[i]])))
}
nodes = data.frame(name = unlist(temp), group = group)
} else if(any(class.object %in% object.pls)) {
w = as.vector(t(mat))
Xn=sum(keep.X) #number of non-zero parameters in X (over all comp)
Yn=sum(keep.Y) #number of non-zero parameters in Y (over all comp)
node.X = row.names#[keep.X]#paste0("X", 1:Xn)
node.Y = col.names#[keep.Y]#paste0("Y", 1:Yn)
row.names.plot = row.names.plot[keep.X]
col.names.plot = col.names.plot[keep.Y]
nodes = data.frame(name = c(node.X, node.Y),
group = c(rep("x", Xn), rep("y", Yn)))
node.X = rep(node.X, each = Yn)
node.Y = rep(node.Y, Xn)
} else {
node.X = row.names # paste0("X", 1:p)
node.Y = col.names # paste0("Y", 1:q)
nodes = data.frame(name = c(node.X, node.Y),
group = c(rep("x", p), rep("y", q)))
node.X = rep(node.X, each = q)
node.Y = rep(node.Y, p)
}
# Definition of edges #
#---------------------#
relations = data.frame(from = node.X, to = node.Y, weight = w)
# edges colors #
#--------------#
id = bin.color(w, cutoff = cutoff, breaks = breaks,
col = color.edge, symkey = symkey)
col.id = id$bin
color.edge = id$col[col.id]
# selection of the edges to incluir in the network #
#--------------------------------------------------#
idx = (abs(w) >= cutoff)
relations = relations[idx, ]
color.edge = color.edge[idx]
# Generation of the graph with all the significant edges #
#--------------------------------------------------------#
gR = graph_from_data_frame(relations, directed = FALSE, vertices = nodes)
# nodes attributes #
#------------------#
V(gR)$label.color = "black"
V(gR)$label.family = "sans"
if(any(class.object %in% object.blocks))
{
V(gR)$label = unlist(block.var.names)
j = 1
for (i in blocks)
{
V(gR)$color[V(gR)$group == i] = color.node[j]
V(gR)$shape[V(gR)$group == i] = shape.node[j]
if (shape.node[j] == "none") {
V(gR)$label.color[V(gR)$group == i] = paste0(substr(color.node[j], 1, 7), "FF")
}
j = j + 1
}
} else {
V(gR)$label = c(row.names.plot, col.names.plot)
V(gR)$color = color.node[1]
V(gR)$color[V(gR)$group == "y"] = color.node[2]
V(gR)$shape = shape.node[1]
if (shape.node[1] == "none") {
V(gR)$label.color = paste0(substr(color.node[1], 1, 7), "FF")
}
V(gR)$shape[V(gR)$group == "y"] = shape.node[2]
if (shape.node[2] == "none") {
V(gR)$label.color[V(gR)$group == "y"] = paste0(substr(color.node[2], 1, 7), "FF")
}
}
# edges attributes #
#------------------#
if (show.edge.labels)
E(gR)$label = round(E(gR)$weight, 2)
E(gR)$label.color = "black"
E(gR)$color = color.edge
#E(gR)$lty = lty.edge
#E(gR)$width = lwd.edge
#from 5.0.x: allow different edge/lwd for >0 and <0 vertices
E(gR)$lty = lty.edge[1]
E(gR)$lty[E(gR)$weight < 0] = lty.edge[2]
E(gR)$width = lwd.edge[1]
E(gR)$width[E(gR)$weight < 0] = lwd.edge[2]
gR = delete_vertices(gR, which(degree(gR) == 0))
# plot attributes #
#-----------------#
lwid = c(keysize[1], 4)
lhei = c(keysize[2], 4)
lmat = matrix(c(1, 2, 3, 4), 2, 2, byrow = TRUE)
nc = length(id$col)
x = seq(0, 1, length = nc + 2)
z.mat = seq(0, 1, length = nc + 1)
z.mat = matrix(z.mat, ncol = 1)
if ((id$lim[1] < -cutoff) & (id$lim[2] < cutoff))
{
xv = c(0, x[nc + 1])
lv = round(c(id$lim[1], -cutoff), 2)
col = c(id$col, "white")
}
if ((id$lim[1] > -cutoff) & (id$lim[2] > cutoff))
{
xv = c(x[2], 1)
lv = round(c(cutoff, id$lim[2]), 2)
col = c("white", id$col)
}
if ((id$lim[1] < -cutoff) & (id$lim[2] > cutoff))
{
idn = max(which(id$breaks < 0))
idp = min(which(id$breaks > 0))
xv = c(0, x[idn + 1], x[idp], 1)
lv = round(c(id$lim[1], -cutoff, cutoff, id$lim[2]), 2)
col = c(id$col[1:idn], "white", id$col[(idn + 1):nc])
}
#-----------------------------------#
# construction of the initial graph #
#-----------------------------------#
nn = vcount(gR)
V(gR)$label.cex = ifelse(is.null(cex.node.name), 1, cex.node.name)
E(gR)$label.cex = min(2.25 * cex.edge.label/log(nn), 1)
cex0 = 2 * V(gR)$label.cex
def.par = par(no.readonly = TRUE)
dev.new()
par(pty = "s", mar = c(0, 0, 0, 0),mfrow=c(1,1))
upr.bnd <- 190*(graph.scale^2) + 10
plot(1:upr.bnd, 1:upr.bnd, type = "n", axes = FALSE, xlab = "", ylab = "")
cha = V(gR)$label
cha = paste("", cha, "")
xh = strwidth(cha, cex = ifelse(size.node==0.5, cex0, size.node*4)) * 1.5 * (2-graph.scale)
yh = strheight(cha, cex = ifelse(size.node==0.5, cex0, size.node*4)) * 3 * (2-graph.scale)
V(gR)$size = xh
V(gR)$size2 = yh
dev.off()
if (is.null(layout.fun))
{
l = layout.fruchterman.reingold(gR, weights = (1 - abs(E(gR)$weight)))
} else {
l = layout.fun(gR)
}
if (isTRUE(!interactive))
{
if (isTRUE(show.color.key))
{
l = layout.fruchterman.reingold(gR, weights = (1 - abs(E(gR)$weight)))
} else {
l = layout.fun(gR)
}
if (isTRUE(!interactive))
{
if (isTRUE(show.color.key))
{
layout(lmat, widths = lwid, heights = lhei, respect = FALSE)
par(mar = c(5, 4, 2, 1), cex = 0.75)
image(z.mat, col = col, xaxt = "n", yaxt = "n")
box()
par(usr = c(0, 1, 0, 1))
axis(1, at = xv, labels = lv, cex.axis = keysize.label)
title("Color key", font.main = 1, cex.main = keysize.label)
par(def.par)
par(new = TRUE)
}
par(pty = "s", mar = c(0, 0, 0, 0),mfrow=c(1,1))
plot(gR, layout = l)
par(def.par)
}
}
#-----------------------#
# procedure interactive #
#-----------------------#
gE.none = FALSE
if (isTRUE(interactive))
{
# cutoff control bar #
#-----------------------#
min.cut = cutoff
max.cut = max(abs(w))
cutoff.old = cutoff
dev.new("width" = 5, "height" = 2.7, xpos = -1)
def.par = par(no.readonly = TRUE)
cuts = seq(0, 1, length = 21)
par(mai = c(0.25, 0.15, 0.3, 0.15), bg = gray(0.95))
layout(matrix(c(0, 1, 0), ncol = 1, nrow = 3),
widths = 1, heights = c(0.25, 1, 0.25))
plot(cuts, type = "n", rep(0, 21), xlab = "", ylab = "",
xlim = c(-0.10, 1.10), axes = FALSE)
title("cutoff control", cex.main = 1.9, font.main = 1)
text(0.5, -0.6, "value", cex = 1.5)
text(0, -0.6, round(min.cut, 2), cex = 1.4)
text(1, -0.6, round(max.cut, 2), cex = 1.4)
mtext(min.cut, side = 1, line = -1, outer = FALSE, cex = 0.95)
rect(-0.1, -0.3, -0.02, 0.3, col = "white")
rect(1.02, -0.3, 1.1, 0.3, col = "white")
points(1.06, 0, pch = 3, cex = 2.4)
lines(c(-0.085, -0.035), c(0, 0))
for (i in seq(0, 1, length = 21))
lines(c(i, i), c(-0.22, 0.2))
x = pos = 0
rect(-0.01, -0.045, x, 0.04, col = "red")
rect(x, -0.045, 1.01, 0.04, col = "white")
bar.dev = dev.cur()
# construction of the initial graph #
#-----------------------------------#
dev.new()
net.dev = dev.cur()
if (isTRUE(show.color.key))
{
layout(lmat, widths = lwid, heights = lhei, respect = FALSE)
par(mar = c(5, 4, 2, 1), cex = 0.75)
image(z.mat, col = col, xaxt = "n", yaxt = "n")
box()
par(usr = c(0, 1, 0, 1))
axis(1, at = xv, labels = lv, cex.axis = keysize.label)
title("Color key", font.main = 1, cex.main = keysize.label)
par(def.par)
par(new = TRUE)
}
par(pty = "s", mar = c(0, 0, 0, 0))
plot(gR, layout = l)
par(def.par)
old.pos = -1
repeat {
dev.set(bar.dev)
z = locator(1, type = "n")
x = z[[1]]
y = z[[2]]
if (is.null(z)) break
if (0 <= x & x <= 1 & -0.22 <= y & y <= 0.22)
{
rect(0, -0.045, x, 0.04, col = "red")
rect(x, -0.045, 1.01, 0.04, col = "white")
pos = x
}
if (1.02 <= x & x <= 1.1 & -0.3 <= y & y <= 0.3)
{
x = pos + 0.05
idx = which.min(abs(cuts - x))
x = cuts[idx]
pos = x
rect(0, -0.045, x, 0.04, col = "red")
rect(x, -0.045, 1.01, 0.04, col = "white")
}
if (-0.1 <= x & x <= -0.02 & -0.3 <= y & y <= 0.3)
{
x = pos - 0.05
idx = which.min(abs(cuts - x))
x = cuts[idx]
pos = x
rect(0, -0.045, x, 0.04, col = "red")
rect(x, -0.045, 1.01, 0.04, col = "white")
}
if (old.pos != pos)
{
old.pos = pos
rect(0.4, -0.8, 0.6, -1.5, col = gray(0.95), border = NA)
cutoff = (max.cut - min.cut) * pos + min.cut
mtext(round(cutoff, 3), side = 1, line = -1, cex = 0.9)
# new graph plot #
#----------------#
dev.set(net.dev)
if (cutoff >= cutoff.old)
{
# selection of the edges to remove of the network #
#-------------------------------------------------#
supp.edge = E(gR)[abs(E(gR)$weight) < cutoff]
# Generation of the graph with all the significant edges #
#--------------------------------------------------------#
gE = delete.edges(gR, supp.edge)
gE = delete.vertices(gE, which(degree(gE) == 0))
# graph plot #
#------------#
nn = vcount(gE)
V(gR)$label.cex = min(2.5 * cex.node.name/log(nn), 1)
E(gR)$label.cex = min(2.25 * cex.edge.label/log(nn), 1)
cex0 = 2 * V(gE)$label.cex
def.par = par(no.readonly = TRUE)
par(pty = "s", mar = c(0, 0, 0, 0))
plot(1:100, 1:100, type = "n", xaxt = "n")
cha = V(gE)$label
cha = paste("", cha, "")
xh = strwidth(cha, cex = cex0) * 1.5
yh = strheight(cha, cex = cex0) * 3
V(gE)$size = xh
V(gE)$size2 = yh
par(def.par)
if (is.null(layout.fun))
{
l = layout.fruchterman.reingold(gE, weights = (1 - abs(E(gE)$weight)))
} else {
l = layout.fun(gE)
}
if (isTRUE(show.color.key))
{
layout(lmat, widths = lwid, heights = lhei, respect = FALSE)
par(mar = c(5, 4, 2, 1), cex = 0.75)
image(z.mat, col = col, xaxt = "n", yaxt = "n")
box()
par(usr = c(0, 1, 0, 1))
axis(1, at = xv, labels = lv, cex.axis = keysize.label)
title("Color key", font.main = 1, cex.main = keysize.label)
par(def.par)
par(new = TRUE)
}
par(pty = "s", mar = c(0, 0, 0, 0))
plot(gE, layout = l)
par(def.par)
cutoff.old = cutoff
} else {
# selection of the edges to incluir in the network #
#--------------------------------------------------#
supp.edge = E(gR)[abs(E(gR)$weight) < cutoff]
# generation of the graph with all the significant edges #
#--------------------------------------------------------#
gE = delete.edges(gR, supp.edge)
gE = delete.vertices(gE, which(degree(gE) == 0))
# graph plot #
#------------#
nn = vcount(gE)
V(gR)$label.cex = min(2.5 * cex.node.name/log(nn), 1)
E(gR)$label.cex = min(2.25 * cex.edge.label/log(nn), 1)
cex0 = 2 * V(gE)$label.cex
def.par = par(no.readonly = TRUE)
par(pty = "s", mar = c(0, 0, 0, 0))
plot(1:100, 1:100, type = "n", xaxt = "n")
cha = V(gE)$label
cha = paste("", cha, "")
xh = strwidth(cha, cex = cex0) * 1.5
yh = strheight(cha, cex = cex0) * 3
V(gE)$size = xh
V(gE)$size2 = yh
par(def.par)
if (is.null(layout.fun))
{
l = layout.fruchterman.reingold(gE, weights = (1 - abs(E(gE)$weight)))
} else {
l = layout.fun(gE)
}
if (isTRUE(show.color.key))
{
layout(lmat, widths = lwid, heights = lhei, respect = FALSE)
par(mar = c(5, 4, 2, 1), cex = 0.75)
image(z.mat, col = col, xaxt = "n", yaxt = "n")
box()
par(usr = c(0, 1, 0, 1))
axis(1, at = xv, labels = lv, cex.axis = keysize.label)
title("Color key", font.main = 1, cex.main = keysize.label)
par(def.par)
par(new = TRUE)
}
par(pty = "s", mar = c(0, 0, 0, 0))
plot(gE, layout = l)
par(def.par)
cutoff.old = cutoff
}
gE.none = TRUE
}
} # end loop
if (gE.none != FALSE)
gR = gE
}
res=list(gR = gR)
if(any(class.object %in% object.blocks))
{
l = 1
for (i in 1:(length(blocks)-1))
{
for (j in (i + 1):length(blocks))
{
M_block[[l]][abs(M_block[[l]]) < cutoff] = 0
res[paste("M",blocks[i],blocks[j],sep="_")] = list(M_block[[l]])
l = l + 1
}
}
} else {
mat[abs(mat) < cutoff] = 0
res$M=mat
}
res$cutoff = cutoff
if (!is.null(save))
dev.off()
return(invisible(res))
}
mixOmicsTeam/mixOmics documentation built on Nov. 4, 2024, 8:56 a.m.
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Defines functions network
Documented in network
#' Relevance Network for (r)CCA and (s)PLS regression
#'
#' Display relevance associations network for (regularized) canonical
#' correlation analysis and (sparse) PLS regression. The function avoids the
#' intensive computation of Pearson correlation matrices on large data set by
#' calculating instead a pair-wise similarity matrix directly obtained from the
#' latent components of our integrative approaches (CCA, PLS, block.pls
#' methods). The similarity value between a pair of variables is obtained by
#' calculating the sum of the correlations between the original variables and
#' each of the latent components of the model. The values in the similarity
#' matrix can be seen as a robust approximation of the Pearson correlation (see
#' González et al. 2012 for a mathematical demonstration and exact formula).
#' The advantage of relevance networks is their ability to simultaneously
#' represent positive and negative correlations, which are missed by methods
#' based on Euclidean distances or mutual information. Those networks are
#' bipartite and thus only a link between two variables of different types can
#' be represented. The network can be saved in a .glm format using the
#' \code{igraph} package, the function \code{write.graph} and extracting the
#' output \code{object$gR}, see details.
#'
#' \code{network} allows to infer large-scale association networks between the
#' \eqn{X} and \eqn{Y} datasets in \code{rcc} or \code{spls}. The output is a
#' graph where each \eqn{X}- and \eqn{Y}-variable corresponds to a node and the
#' edges included in the graph portray associations between them.
#'
#' In \code{rcc}, to identify \eqn{X}-\eqn{Y} pairs showing relevant
#' associations, \code{network} calculate a similarity measure between \eqn{X}
#' and \eqn{Y} variables in a pair-wise manner: the scalar product value
#' between every pairs of vectors in dimension \code{length(comp)} representing
#' the variables \eqn{X} and \eqn{Y} on the axis defined by \eqn{Z_i} with
#' \eqn{i} in \code{comp}, where \eqn{Z_i} is the equiangular vector between
#' the \eqn{i}-th \eqn{X} and \eqn{Y} canonical variate.
#'
#' In \code{spls}, if \code{object$mode} is \code{regression}, the similarity
#' measure between \eqn{X} and \eqn{Y} variables is given by the scalar product
#' value between every pairs of vectors in dimension \code{length(comp)}
#' representing the variables \eqn{X} and \eqn{Y} on the axis defined by
#' \eqn{U_i} with \eqn{i} in \code{comp}, where \eqn{U_i} is the \eqn{i}-th
#' \eqn{X} variate. If \code{object$mode} is \code{canonical} then \eqn{X} and
#' \eqn{Y} are represented on the axis defined by \eqn{U_i} and \eqn{V_i}
#' respectively.
#'
#' Variable pairs with a high similarity measure (in absolute value) are
#' considered as relevant. By changing the cut-off, one can tune the relevance
#' of the associations to include or exclude relationships in the network.
#'
#' \code{interactive=TRUE} open two device, one for association network, one
#' for scrollbar, and define an interactive process: by clicking either at each
#' end (\eqn{-} or \eqn{+}) of the scrollbar or at middle portion of this.
#' The position of the slider indicate which is the `cutoff' value associated
#' to the display network.
#'
#' The network can be saved in a .glm format using the \pkg{igraph} package,
#' the function \code{write.graph} and extracting the output \code{obkect$gR}.
#'
#' The interactive process is terminated by clicking the second button and
#' selecting \code{Stop} from the menu, or from the \code{Stop} menu on the graphics
#' window.
#'
#' The \code{color.node} is a vector of length two, of any of the three kind of
#' \code{R} colors, i.e., either a color name (an element of \code{colors()}),
#' a hexadecimal string of the form \code{"#rrggbb"}, or an integer \code{i}
#' meaning \code{palette()[i]}. \code{color.node[1]} and \code{color.node[2]}
#' give the color for filled nodes of the \eqn{X}- and \eqn{Y}-variables
#' respectively. Defaults to \code{c("white", "white")}.
#'
#' \code{color.edge} give the color to edges with colors corresponding to the
#' values in \code{mat}. Defaults to \code{color.GreenRed(100)} for negative
#' (green) and positive (red) correlations. We also propose other palettes of
#' colors, such as \code{color.jet} and \code{color.spectral}, see help on
#' those functions, and examples below. Other palette of colors from the stats
#' package can be used too.
#'
#' \code{shape.node[1]} and \code{shape.node[2]} provide the shape of the nodes
#' associate to \eqn{X}- and \eqn{Y}-variables respectively. Current acceptable
#' values are \code{"circle"} and \code{"rectangle"}. Defaults to
#' \code{c("circle", "rectangle")}.
#'
#' \code{lty.edge[1]} and \code{lty.egde[2]} give the line type to edges with
#' positive and negative weight respectively. Can be one of \code{"solid"},
#' \code{"dashed"}, \code{"dotted"}, \code{"dotdash"}, \code{"longdash"} and
#' \code{"twodash"}. Defaults to \code{c("solid", "solid")}.
#'
#' \code{lwd.edge[1]} and \code{lwd.edge[2]} provide the line width to edges
#' with positive and negative weight respectively. This attribute is of type
#' double with a default of \code{c(1, 1)}.
#'
#' @aliases network network.default network.rcc network.pls network.spls
#' @param mat numeric matrix of values to be represented. Alternatively,
#' an object from one of the following models: \code{mix_pls}, \code{plsda},
#' \code{mixo_spls}, \code{splsda}, \code{rcc}, \code{sgcca}, \code{rgcca},
#' \code{sgccda}.
#' @param comp atomic or vector of positive integers. The components to
#' adequately account for the data association. Defaults to \code{comp = 1}.
#' @param cutoff numeric value between \code{0} and \code{1}. The tuning
#' threshold for the relevant associations network (see Details).
#' @param row.names,col.names character vector containing the names of \eqn{X}-
#' and \eqn{Y}-variables.
#' @param graph.scale Numeric between 0 and 1 which alters the scale of the entire
#' plot. Increasing the value decreases the size of nodes and increases their distance
#' from one another. Defaults to 0.5.
#' @param size.node Numeric between 0 and 1 which determines the relative size of nodes.
#' Defaults to 0.5.
#' @param color.node vector of length two, the colors of the \eqn{X} and
#' \eqn{Y} nodes (see Details).
#' @param shape.node character vector of length two, the shape of the \eqn{X}
#' and \eqn{Y} nodes (see Details).
#' @param alpha.node Numeric between 0 and 1 which determines the opacity of nodes.
#' Only used in block objects.
#' @param color.edge vector of colors or character string specifying the colors
#' function to using to color the edges, set to default to
#' \code{color.GreenRed(100)} but other palettes can be chosen (see Details and
#' Examples).
#' @param lty.edge character vector of length two, the line type for the edges
#' (see Details).
#' @param lwd.edge vector of length two, the line width of the edges (see
#' Details).
#' @param show.edge.labels logical. If \code{TRUE}, plot association values as
#' edge labels (defaults to \code{FALSE}).
#' @param show.color.key Logical. If \code{TRUE} a color key should be plotted.
#' @param symkey Logical indicating whether the color key should be made
#' symmetric about 0. Defaults to \code{TRUE}.
#' @param keysize numeric value indicating the size of the color key.
#' @param keysize.label vector of length 1, indicating the size of the labels
#' and title of the color key.
#' @param breaks (optional) either a numeric vector indicating the splitting
#' points for binning \code{mat} into colors, or a integer number of break
#' points to be used, in which case the break points will be spaced equally
#' between \code{min(mat)} and \code{max(mat)}.
#' @param interactive logical. If \code{TRUE}, a scrollbar is created to change
#' the cutoff value interactively (defaults to \code{FALSE}). See Details.
#' @param save should the plot be saved ? If so, argument to be set either to
#' \code{'jpeg'}, \code{'tiff'}, \code{'png'} or \code{'pdf'}.
#' @param name.save character string giving the name of the saved file.
#' @param cex.edge.label the font size for the edge labels.
#' @param cex.node.name the font size for the node labels.
#' @param blocks a vector indicating the block variables to display.
#' @param block.var.names either a list of vector components for variable names
#' in each block or FALSE for no names. If TRUE, the columns names of the
#' blocks are used as names.
#' @param layout.fun a function. It specifies how the vertices will be placed
#' on the graph. See help(layout) in the igraph package. Defaults to
#' layout.fruchterman.reingold.
#' @param plot.graph logical. If \code{TRUE} (default), plotting window will be
#' filled with network. If \code{FALSE}, then no graph will be plotted, though
#' the return value of the function is the exact same.
#' @return \code{network} return a list containing the following components:
#' \item{M}{the correlation matrix used by \code{network}.} \item{gR}{a
#' \code{graph} object to save the graph for cytoscape use (requires to load
#' the \pkg{igraph} package).}
#' @section Warning: If the number of variables is high, the generation of the
#' network generation can take some time.
#' @author Ignacio González, Kim-Anh Lê Cao, AL J Abadi
#' @seealso \code{\link{plotVar}}, \code{\link{cim}},
#' \code{\link{color.GreenRed}}, \code{\link{color.jet}},
#' \code{\link{color.spectral}} and http: //www.mixOmics.org for more details.
#' @references Mathematical definition: González I., Lê Cao K-A., Davis, M.J.
#' and Déjean, S. (2012). Visualising associations between paired omics data
#' sets. J. Data Mining 5:19.
#' \url{http://www.biodatamining.org/content/5/1/19/abstract}
#'
#' Examples and illustrations:
#'
#' Rohart F, Gautier B, Singh A, Lê Cao K-A. mixOmics: an R package for 'omics
#' feature selection and multiple data integration. PLoS Comput Biol 13(11):
#' e1005752
#'
#' Relevance networks:
#'
#' Butte, A. J., Tamayo, P., Slonim, D., Golub, T. R. and Kohane, I. S. (2000).
#' Discovering functional relationships between RNA expression and
#' chemotherapeutic susceptibility using relevance networks. \emph{Proceedings
#' of the National Academy of Sciences of the USA} \bold{97}, 12182-12186.
#'
#' Moriyama, M., Hoshida, Y., Otsuka, M., Nishimura, S., Kato, N., Goto, T.,
#' Taniguchi, H., Shiratori, Y., Seki, N. and Omata, M. (2003). Relevance
#' Network between Chemosensitivity and Transcriptome in Human Hepatoma Cells.
#' \emph{Molecular Cancer Therapeutics} \bold{2}, 199-205.
#' @keywords multivariate graphs dplot hplot iplot
#' @export
#' @example ./examples/network-examples.R
network <- function(mat,
comp = NULL,
blocks = c(1, 2),
cutoff = 0,
row.names = TRUE,
col.names = TRUE,
block.var.names = TRUE,
graph.scale = 0.5,
size.node = 0.5,
color.node = NULL,
shape.node = NULL,
alpha.node = 0.85,
cex.node.name = NULL,
color.edge = color.GreenRed(100),
lty.edge = "solid",
lwd.edge = 1,
show.edge.labels = FALSE,
cex.edge.label = 1,
show.color.key = TRUE,
symkey = TRUE,
keysize = c(1, 1),
keysize.label = 1,
breaks,
interactive = FALSE,
layout.fun = NULL,
save = NULL,
name.save = NULL,
plot.graph = TRUE
)
{
#-- checking general input parameters --------------------------------------#
#---------------------------------------------------------------------------#
#-- check that the user did not enter extra arguments
arg.call = match.call()
user.arg = names(arg.call)[-1]
err = tryCatch(mget(names(formals()), sys.frame(sys.nframe())),
error = function(e) e)
if ("simpleError" %in% class(err))
stop(err[[1]], ".", call. = FALSE)
function.arg = names(mget(names(formals()), sys.frame(sys.nframe())))
not.arg = !(user.arg %in% function.arg)
if (any(not.arg))
{
unused.arg = user.arg[not.arg]
not.arg = which(not.arg) + 1
output = rep("", length(not.arg))
for (i in 1:length(not.arg))
{
output[i] = paste0(unused.arg[i], " = ", arg.call[[not.arg[i]]])
}
output = paste0("(", paste(output, collapse = ", "), ").")
msg = "unused argument "
if (length(not.arg) > 1) msg = "unused arguments "
stop(msg, output, call. = FALSE)
}
# #-- check blocks
# if(length(blocks) != 2)
# stop("We can only display 2 blocks",call.=FALSE)
#-- save
if (!is.null(save))
{
if (! save %in% c("jpeg","tiff","png","pdf"))
stop("'save' must be one of 'jpeg', 'png', 'tiff' or 'pdf'.", call. = FALSE)
}
#-- name.save
if (!is.null(name.save))
{
if (! is.character(name.save) || length(name.save) > 1)
stop("'name.save' must be a character.", call. = FALSE)
} else {
if (!is.null(save))
name.save = paste0("network_",gsub(".", "_", deparse(substitute(mat)) ,fixed = TRUE))
}
if (!is.null(save)){
while (dev.cur()>1)
dev.off()
if (save == "jpeg")
jpeg(filename = paste0(name.save,".jpeg"), res = 600, width = 4000, height = 4000)
if (save == "png")
jpeg(filename = paste0(name.save,".png"), res = 600, width = 4000, height = 4000)
if (save == "tiff")
tiff(filename = paste0(name.save,".tiff"), res = 600, width = 4000, height = 4000)
if (save == "pdf")
pdf(file = paste0(name.save,".pdf"))
}
if (!plot.graph & interactive) {
stop("plot.graph cannot be FALSE if interactive = TRUE", call.=FALSE)
}
class.object = class(mat)
object.pls=c("mixo_pls","mixo_spls","mixo_mlspls")
object.rcc="rcc"
object.blocks=c("sgcca","rgcca")
if (! any(class.object %in% c(object.pls,object.rcc,object.blocks, "matrix")))
stop( " 'network' is only implemented for the following objects: matrix, pls, plsda, spls, splsda, rcc, sgcca, rgcca, sgccda", call.=FALSE)
if(any(class.object %in% c(object.rcc,object.pls)))
{
p = ncol(mat$X)
if(any(class.object == "DA")) # object is DA
mat$Y = mat$ind.mat
q = ncol(mat$Y)
n = nrow(mat$X)
ncomp = mat$ncomp
#-- comp
if(is.null(comp))
comp=1:mat$ncomp
if (length(comp) == 1)
{
if(comp>ncomp)
{
stop("the elements of 'comp' must be smaller than or equal to ", ncomp, ".",
call. = FALSE)
} else if ( !is.numeric(comp) || comp <= 0) {
stop("invalid value for 'comp'.", call. = FALSE)
}
}
if (length(comp) > 1)
{
if(length(comp) > ncomp)
stop("the length of 'comp' must be smaller than or equal to ", ncomp, ".",
call. = FALSE)
if (!is.numeric(comp) || any(comp < 1))
stop("invalid vector for 'comp'.", call. = FALSE)
if (any(comp > ncomp))
stop("the elements of 'comp' must be <= ", ncomp, ".",
call. = FALSE)
}
comp = round(comp)
#-- row.names
row.names.plot = TRUE # whether to plot the label in the graph
if (is.logical(row.names))
{
if(!isTRUE(row.names))
{
row.names.plot = FALSE
}
row.names = mat$names$colnames$X
} else {
row.names = as.vector(row.names)
if (length(unique(row.names)) != p)
stop("'row.names' must be a character vector of ", p, " unique entries.",
call. = FALSE)
}
if(row.names.plot == TRUE)
{
row.names.plot = row.names
}else{
row.names.plot = rep("",p)
}
#-- col.names
col.names.plot = TRUE # whether to plot the label in the graph
if (is.logical(col.names))
{
if(!isTRUE(col.names))
{
col.names.plot = FALSE
}
col.names = mat$names$colnames$Y
} else {
col.names = as.vector(col.names)
if (length(col.names) != q)
stop("'col.names' must be a character vector of ", q, " unique entries.",
call. = FALSE)
}
if(col.names.plot == TRUE)
{
col.names.plot = col.names
}else{
col.names.plot = rep("",q)
}
#-- end checking --#
#------------------#
#-- network ----------------------------------------------------------------#
#---------------------------------------------------------------------------#
if(any(class.object %in% object.rcc))
{
#-- similarity matrix --#
bisect = mat$variates$X[, comp] + mat$variates$Y[, comp]
cord.X = cor(mat$X, bisect, use = "pairwise")
cord.Y = cor(mat$Y, bisect, use = "pairwise")
mat = cord.X %*% t(cord.Y)
} else if(any(class.object %in% object.pls)) {
#-- variable selection --#
if (all(class(mat) %in% "mixo_pls"))
{
keep.X = rep(TRUE,p)
keep.Y = rep(TRUE,q)
} else {
keep.X = apply(abs(mat$loadings$X[, comp, drop=FALSE]), 1, sum) > 0
keep.Y = apply(abs(mat$loadings$Y[, comp, drop=FALSE]), 1, sum) > 0
row.names = row.names[keep.X]
col.names = col.names[keep.Y]
}
#-- similarity matrix --#
if (mat$mode == "canonical")
{
cord.X = cor(mat$X[, keep.X], mat$variates$X[, comp], use = "pairwise")
cord.Y = cor(mat$Y[, keep.Y], mat$variates$Y[, comp], use = "pairwise")
} else {
cord.X = cor(mat$X[, keep.X], mat$variates$X[, comp], use = "pairwise")
cord.Y = cor(mat$Y[, keep.Y], mat$variates$X[, comp], use = "pairwise")
}
mat = cord.X %*% t(cord.Y)
}
} else if(any(class.object %in% object.blocks)) {
mat$X <- mapply(mat$X, names(mat$X), FUN = function(x, y)
{
colnames(x) <- paste0(colnames(x),"_", y)
x
}, SIMPLIFY = FALSE)
# remove Y from the list of blocks for DA objects
if(any(class.object == "DA"))
{
mat$names$blocks = mat$names$blocks [-mat$indY]
mat$names$colnames = mat$names$colnames [-mat$indY]
mat$ncomp = mat$ncomp [-mat$indY]
}
if (is.null(blocks))
{
if (any(mat$ncomp > 1))
{
blocks = mat$names$blocks[ which(mat$ncomp > 1)]
} else {
stop(("The number of components for each block is 1. The number of components must be superior or equal to 2."), call. = FALSE)
}
} else if (is.numeric(blocks) & min(blocks) > 0 & max(blocks) <= length(mat$names$blocks)) {
blocks = mat$names$blocks[blocks]
} else if (is.character(blocks)) {
if (!all(blocks %in% mat$names$blocks))
stop("One element of 'blocks' does not match with the names of the blocks")
} else {
stop("Incorrect value for 'blocks", call. = FALSE)
}
#-- comp
if (is.null(comp))
{
comp = vector("list", length(blocks))
names(comp) = blocks
for (i in blocks)
comp[[i]] = 1:mat$ncomp[i]
}
if (is.list(comp))
{
if (length(comp) != length(blocks))
stop("'comp' must be either NULL a list of length ", length(blocks), ".",
call. = FALSE)
if (!all(blocks %in% names(comp)))
stop("names of 'comp' must be from {",
paste(blocks, collapse = ", "), "}.", call. = FALSE)
for (i in blocks)
{
if (any(!is.finite(comp[[i]])))
stop("invalid value for 'comp' of the block '", i, "'.", call. = FALSE)
if (any(comp[[i]] > mat$ncomp[i]))
stop("the elements of 'comp' for block '", i, "' must be <= ",
mat$ncomp[i], ".", call. = FALSE)
if (any(comp[[i]] < 1))
stop("invalid value for 'comp' of the block '", i, "'.", call. = FALSE)
}
} else {
stop("'comp' must be either NULL or a list of length ", length(blocks), ".",
call. = FALSE)
}
#-- block.var.names
num.var = unlist(lapply(mat$X[blocks], ncol))
if (is.logical(block.var.names))
{
if (length(block.var.names)==1)
block.var.names=rep(block.var.names,length(blocks))
if (length(block.var.names) != length(blocks))
stop("'block.var.names' must be a logical vector of length 1 or ", length(blocks),", or a list of length ", length(blocks), ".",
call. = FALSE)
vec=(which(block.var.names==FALSE))
block.var.names = mat$names$colnames
for (i in 1:length(blocks))
{
if (i %in% vec)
block.var.names[[blocks[i]]] = rep(" ",length(mat$names$colnames[[blocks[i]]]))
}
} else {
if (is.list(block.var.names))
{
if (length(block.var.names) != length(blocks))
{
stop("'block.var.names' must be a logical vector or a list of length ", length(blocks), ".",
call. = FALSE)
} else {
if (!all(unlist(lapply(block.var.names, is.vector))))
stop("each component of 'block.var.names' must be a vector.", call. = FALSE)
block.var.names.length = unlist(lapply(block.var.names, length))
if (any(block.var.names.length != num.var))
stop("components of 'block.var.names' must be vectors of length ",
paste(num.var, collapse = ", "), ".", call. = FALSE)
}
} else {
stop("'block.var.names' must be either a logical value or a list of length ",
length(blocks), ".", call. = FALSE)
}
}
#-- network approach -------------------------------------------------------#
#---------------------------------------------------------------------------#
#-- calculation of the similarity matrix for each block --#
coord = M_block = list()
j = 1
if (is(mat, "sgcca"))
{
for (k in blocks)
{
if (length(comp[[k]]) > 1)
{
keep = (apply(abs(mat$loadings[[k]][, comp[[k]]]), 1, sum) > 0)
} else {
keep = abs(mat$loadings[[k]][, comp[[k]]]) > 0
}
coord[[j]] = cor(mat$X[[k]][, keep], mat$variates[[k]][, comp[[k]]], use = "pairwise")
j = j + 1
}
} else {
for(k in blocks)
{
coord[[j]] = cor(mat$X[[k]], mat$variates[[k]][, comp[[k]]], use = "pairwise")
j = j + 1
}
}
node.X = node.Y = w = NULL
l = 1
for (j in 1:(length(blocks) - 1))
{
for (k in (j + 1):length(blocks))
{
if(!any(comp[[blocks[j]]] %in% comp[[blocks[k]]]))
stop("comp of block ",blocks[j], " is ", comp[[blocks[j]]], " but comp of block ", blocks[k]," is ",comp[[blocks[k]]],
call. = FALSE)
int.comp = intersect(comp[[blocks[j]]], comp[[blocks[k]]])
object = coord[[j]][, comp[[blocks[j]]] %in% int.comp] %*% t(coord[[k]][, comp[[blocks[k]]] %in% int.comp])
M_block[[l]] = object
l = l + 1
X = rownames(coord[[j]])
Y = rownames(coord[[k]])
rep.X = rep(X, each = length(Y))
rep.Y = rep(Y, length(X))
node.X = c(node.X, rep.X)
node.Y = c(node.Y, rep.Y)
w = c(w, as.vector(t(object)))
}
}
} else {
#-- mat
if (!is.matrix(mat))
stop("'mat' must be a numeric matrix.", call. = FALSE)
if (length(dim(mat)) != 2)
stop("'mat' must be a numeric matrix.")
if (!is.numeric(mat))
stop("'mat' must be a numeric matrix.")
p = nrow(mat)
q = ncol(mat)
#-- row.names
row.names.plot = TRUE # whether to plot the label in the graph
if (is.logical(row.names))
{
if(!isTRUE(row.names))
{
row.names.plot = FALSE
}
row.names = rownames(mat)
} else {
row.names = as.vector(row.names)
if (length(row.names) != p)
stop("'row.names' must be a character vector of ", p, " unique entries.",
call. = FALSE)
}
if(row.names.plot == TRUE)
{
row.names.plot = row.names
}else{
row.names.plot = rep("",p)
}
#-- col.names
col.names.plot = TRUE # whether to plot the label in the graph
if (is.logical(col.names))
{
if(!isTRUE(col.names))
{
col.names.plot = FALSE
}
col.names = colnames(mat)
} else {
col.names = as.vector(col.names)
if (length(col.names) != q)
stop("'col.names' must be a character vector of ", q, " unique entries.",
call. = FALSE)
}
if(col.names.plot == TRUE)
{
col.names.plot = col.names
}else{
col.names.plot = rep("",q)
}
}
#-- size.node
if (!is.null(size.node)) {
if (!is.finite(size.node) || size.node < 0 || size.node > 1) {
stop("'size.node' must be a numerical value between 0 - 1.", call. = FALSE)
}
if (size.node == 0) {
shape.node <- "none"
size.node <- 1 # prevents error
}
}
#-- graph.scale
if (!is.finite(graph.scale) || graph.scale < 0 || graph.scale > 1) {
stop("'graph.scale' must be a numerical value between 0 - 1.", call. = FALSE)
}
#-- color.node
if(any(class.object %in% object.blocks))
{
if (is.null(color.node))
{
## see circosPlot
color.blocks = brewer.pal(n = 12, name = 'Paired') #why 12?? ANS: bc max allowed n is 12 for this function
if (length(blocks) > 6) {
color.blocks <- colorRampPalette(color.blocks)(2*length(object$X))
}
color.node = color.blocks[seq(from = 1, to = 2*length(blocks), by = 2)]
color.node = adjustcolor(color.node, alpha.f = alpha.node)
names(color.node) = blocks
} else {
if (!is.vector(color.node) || length(color.node) != length(blocks))
stop("'color.node' must be a vector of length ", length(blocks), ".", call. = FALSE)
}
} else {
if(is.null(color.node))
color.node = brewer.pal(n = 12, name = 'Paired')[c(1,3)]
color.node = adjustcolor(color.node, alpha.f = alpha.node)
if (!is.list(color.node))
{
if (!is.vector(color.node) || length(color.node) != 2)
stop("'color.node' must be a vector of length 2.", call. = FALSE)
} else {
stop("'color.node' must be a vector of length 2.", call. = FALSE)
}
}
if (any(!sapply(color.node, function(x){tryCatch(is.matrix(col2rgb(x)), error = function(e) FALSE) })))
stop("'color.node' must be a character vector of recognized colors.",
call. = FALSE)
#-- shape.node
if(any(class.object%in% object.blocks))
{
if (is.null(shape.node))
shape.node = "circle"
if (is.vector(shape.node))
{
if (length(shape.node) == 1)
shape.node = rep(shape.node, length(blocks))
}
if (!is.list(shape.node))
{
if (!is.vector(shape.node) || length(shape.node) != length(blocks))
stop("'shape.node' must be a character vector of length ", length(blocks), ".",
call. = FALSE)
} else {
stop("'shape.node' must be a numeric vector of length ", length(blocks), ".",
call. = FALSE)
}
if (!all(shape.node %in% c("none", "circle", "rectangle")))
stop("elements of 'shape.node' must be from {'none', 'circle', 'rectangle'}.",
call. = FALSE)
if (is.null(names(shape.node)))
names(shape.node) = blocks
} else {
if(is.null(shape.node))
shape.node=c("circle", "rectangle")
if (length(shape.node)==1) {
if(shape.node=="none") {
shape.node=c("none", "none")
}
}
if (!is.list(shape.node))
{
if (!is.vector(shape.node) || length(shape.node) != 2)
stop("'shape.node' must be a vector of length 2.", call. = FALSE)
} else {
stop("'shape.node' must be a vector of length 2.", call. = FALSE)
}
if (!all(shape.node %in% c("none", "circle", "rectangle")))
stop("elements of 'shape.node' must be from {'none', 'circle', 'rectangle'}.",
call. = FALSE)
}
#-- cex.node.name
if (!is.null(cex.node.name)) {
if (!is.finite(cex.node.name) || cex.node.name < 0 || length(cex.node.name)>1) {
stop("'cex.node.name' must be a non-negative numerical value.", call. = FALSE)
}
}
#-- color.edge
if (length(color.edge) < 2 && (!is(color.edge, "function")))
stop("'color.edge' must be a vector of length larger than or equal to 2.", call. = FALSE)
if ((length(color.edge) %% 2) != 0 && (!is(color.edge, "function")) && isTRUE(symkey))
stop("'color.edge' must be a vector of length an even number if 'symkey = TRUE'.", call. = FALSE)
if (any(!sapply(color.edge, function(x) {tryCatch(is.matrix(col2rgb(x)), error = function(e) FALSE) })))
stop("'color.edge' must be a character vector of recognized colors.", call. = FALSE)
#-- lty.edge
if(length(lty.edge) >2)
stop("\"lty.edge\" must a character vector of up to 2 entries from
'solid', 'dashed', 'dotted', 'dotdash', 'longdash', twodash' or 'blank'.
see ?network",
call.=FALSE)
if (length(lty.edge)==1) lty.edge = c(lty.edge, lty.edge)
choices = c("solid", "dashed", "dotted", "dotdash", "longdash", "twodash", "blank")
lty.edge = choices[pmatch(lty.edge, choices,duplicates.ok=TRUE)]
if (any(is.na(lty.edge)))
stop("'lty.edge' should be from 'solid', 'dashed', 'dotted', 'dotdash', 'longdash', twodash' or 'blank'.",
call. = FALSE)
#-- lwd.edge
if(length(lwd.edge) >2)
stop("'lwd.edge' must be a vector of up to 2 positive numbers.
See ?network")
if (length(lwd.edge)==1)
lwd.edge = c(lwd.edge, lwd.edge)
if (length(lwd.edge) != 2 || any(!is.finite(lwd.edge)) || any(lwd.edge <= 0))
stop("'lwd.edge' must be positive.")
#-- show.edge.labels
if (!is.logical(show.edge.labels))
stop("'show.edge.labels' must be a logical constant (TRUE or FALSE).",
call. = FALSE)
#-- cex.edge.label
if (!is.finite(cex.edge.label) || cex.edge.label < 0 || length(cex.edge.label)>1)
stop("'cex.edge.label' must be a non-negative numerical value.", call. = FALSE)
#-- show.color.key
if (!is.logical(show.color.key))
stop("'show.color.key' must be a logical constant (TRUE or FALSE).",
call. = FALSE)
#-- symkey
if (!is.logical(symkey))
stop("'symkey' must be a logical constant (TRUE or FALSE).",
call. = FALSE)
#-- keysize
if (length(keysize) != 2 || any(!is.finite(keysize)))
stop("'keysize' must be a numeric vector of length 2.",
call. = FALSE)
#-- keysize.label
if (length(keysize.label) != 1 || any(!is.finite(keysize)))
stop("'keysize' must be a numeric vector of length 1.",
call. = FALSE)
#-- interactive
if (!is.logical(interactive))
stop("'interactive' must be a logical constant (TRUE or FALSE).",
call. = FALSE)
#-- layout.fun
if (!is.null(layout.fun) && !is(layout.fun, "function"))
stop("'layout.fun' must be a valid layout function.", call. = FALSE)
#-- end checking --#
#------------------#
#-- network approach -------------------------------------------------------#
#---------------------------------------------------------------------------#
if (!(any(class.object %in% object.blocks)))
w = as.vector(t(mat))
#-- check cutoff
if (round(max(abs(w)), 2) == 0)
stop("There is no correlation between these blocks whith these components.",
"Try a different value of 'comp'.", call. = FALSE)
if (!is.numeric(cutoff) || cutoff < 0 || cutoff > 1)
stop("'cutoff' should be a numeric between 0 and 1", call. = FALSE)
if(cutoff > max(abs(w)))
stop("You have chosen a high cutoff value of ", cutoff,
" which is greaer than the max value in the similarity matrix which is ",
round(max(abs(w)), 2), call. = FALSE)
# Definition of nodes #
#---------------------#
#save(list=ls(),file="temp.Rdata")
if(any(class.object %in% object.blocks))
{
group = NULL
temp = lapply(mat$X, function(x) colnames(x))
for (i in 1:length(temp))
{
group = c(group, rep(names(temp)[i], length(temp[[i]])))
}
nodes = data.frame(name = unlist(temp), group = group)
} else if(any(class.object %in% object.pls)) {
w = as.vector(t(mat))
Xn=sum(keep.X) #number of non-zero parameters in X (over all comp)
Yn=sum(keep.Y) #number of non-zero parameters in Y (over all comp)
node.X = row.names#[keep.X]#paste0("X", 1:Xn)
node.Y = col.names#[keep.Y]#paste0("Y", 1:Yn)
row.names.plot = row.names.plot[keep.X]
col.names.plot = col.names.plot[keep.Y]
nodes = data.frame(name = c(node.X, node.Y),
group = c(rep("x", Xn), rep("y", Yn)))
node.X = rep(node.X, each = Yn)
node.Y = rep(node.Y, Xn)
} else {
node.X = row.names # paste0("X", 1:p)
node.Y = col.names # paste0("Y", 1:q)
nodes = data.frame(name = c(node.X, node.Y),
group = c(rep("x", p), rep("y", q)))
node.X = rep(node.X, each = q)
node.Y = rep(node.Y, p)
}
# Definition of edges #
#---------------------#
relations = data.frame(from = node.X, to = node.Y, weight = w)
# edges colors #
#--------------#
id = bin.color(w, cutoff = cutoff, breaks = breaks,
col = color.edge, symkey = symkey)
col.id = id$bin
color.edge = id$col[col.id]
# selection of the edges to incluir in the network #
#--------------------------------------------------#
idx = (abs(w) >= cutoff)
relations = relations[idx, ]
color.edge = color.edge[idx]
# Generation of the graph with all the significant edges #
#--------------------------------------------------------#
gR = graph_from_data_frame(relations, directed = FALSE, vertices = nodes)
# nodes attributes #
#------------------#
V(gR)$label.color = "black"
V(gR)$label.family = "sans"
if(any(class.object %in% object.blocks))
{
V(gR)$label = unlist(block.var.names)
j = 1
for (i in blocks)
{
V(gR)$color[V(gR)$group == i] = color.node[j]
V(gR)$shape[V(gR)$group == i] = shape.node[j]
if (shape.node[j] == "none") {
V(gR)$label.color[V(gR)$group == i] = paste0(substr(color.node[j], 1, 7), "FF")
}
j = j + 1
}
} else {
V(gR)$label = c(row.names.plot, col.names.plot)
V(gR)$color = color.node[1]
V(gR)$color[V(gR)$group == "y"] = color.node[2]
V(gR)$shape = shape.node[1]
if (shape.node[1] == "none") {
V(gR)$label.color = paste0(substr(color.node[1], 1, 7), "FF")
}
V(gR)$shape[V(gR)$group == "y"] = shape.node[2]
if (shape.node[2] == "none") {
V(gR)$label.color[V(gR)$group == "y"] = paste0(substr(color.node[2], 1, 7), "FF")
}
}
# edges attributes #
#------------------#
if (show.edge.labels)
E(gR)$label = round(E(gR)$weight, 2)
E(gR)$label.color = "black"
E(gR)$color = color.edge
#E(gR)$lty = lty.edge
#E(gR)$width = lwd.edge
#from 5.0.x: allow different edge/lwd for >0 and <0 vertices
E(gR)$lty = lty.edge[1]
E(gR)$lty[E(gR)$weight < 0] = lty.edge[2]
E(gR)$width = lwd.edge[1]
E(gR)$width[E(gR)$weight < 0] = lwd.edge[2]
gR = delete_vertices(gR, which(degree(gR) == 0))
# plot attributes #
#-----------------#
lwid = c(keysize[1], 4)
lhei = c(keysize[2], 4)
lmat = matrix(c(1, 2, 3, 4), 2, 2, byrow = TRUE)
nc = length(id$col)
x = seq(0, 1, length = nc + 2)
z.mat = seq(0, 1, length = nc + 1)
z.mat = matrix(z.mat, ncol = 1)
if ((id$lim[1] < -cutoff) & (id$lim[2] < cutoff))
{
xv = c(0, x[nc + 1])
lv = round(c(id$lim[1], -cutoff), 2)
col = c(id$col, "white")
}
if ((id$lim[1] > -cutoff) & (id$lim[2] > cutoff))
{
xv = c(x[2], 1)
lv = round(c(cutoff, id$lim[2]), 2)
col = c("white", id$col)
}
if ((id$lim[1] < -cutoff) & (id$lim[2] > cutoff))
{
idn = max(which(id$breaks < 0))
idp = min(which(id$breaks > 0))
xv = c(0, x[idn + 1], x[idp], 1)
lv = round(c(id$lim[1], -cutoff, cutoff, id$lim[2]), 2)
col = c(id$col[1:idn], "white", id$col[(idn + 1):nc])
}
#-----------------------------------#
# construction of the initial graph #
#-----------------------------------#
nn = vcount(gR)
V(gR)$label.cex = ifelse(is.null(cex.node.name), 1, cex.node.name)
E(gR)$label.cex = min(2.25 * cex.edge.label/log(nn), 1)
cex0 = 2 * V(gR)$label.cex
def.par = par(no.readonly = TRUE)
dev.new()
par(pty = "s", mar = c(0, 0, 0, 0),mfrow=c(1,1))
upr.bnd <- 190*(graph.scale^2) + 10
plot(1:upr.bnd, 1:upr.bnd, type = "n", axes = FALSE, xlab = "", ylab = "")
cha = V(gR)$label
cha = paste("", cha, "")
xh = strwidth(cha, cex = ifelse(size.node==0.5, cex0, size.node*4)) * 1.5 * (2-graph.scale)
yh = strheight(cha, cex = ifelse(size.node==0.5, cex0, size.node*4)) * 3 * (2-graph.scale)
V(gR)$size = xh
V(gR)$size2 = yh
dev.off()
if (is.null(layout.fun))
{
l = layout.fruchterman.reingold(gR, weights = (1 - abs(E(gR)$weight)))
} else {
l = layout.fun(gR)
}
if (isTRUE(!interactive))
{
if (isTRUE(show.color.key))
{
l = layout.fruchterman.reingold(gR, weights = (1 - abs(E(gR)$weight)))
} else {
l = layout.fun(gR)
}
if (isTRUE(!interactive))
{
if (isTRUE(show.color.key))
{
layout(lmat, widths = lwid, heights = lhei, respect = FALSE)
par(mar = c(5, 4, 2, 1), cex = 0.75)
image(z.mat, col = col, xaxt = "n", yaxt = "n")
box()
par(usr = c(0, 1, 0, 1))
axis(1, at = xv, labels = lv, cex.axis = keysize.label)
title("Color key", font.main = 1, cex.main = keysize.label)
par(def.par)
par(new = TRUE)
}
par(pty = "s", mar = c(0, 0, 0, 0),mfrow=c(1,1))
plot(gR, layout = l)
par(def.par)
}
}
#-----------------------#
# procedure interactive #
#-----------------------#
gE.none = FALSE
if (isTRUE(interactive))
{
# cutoff control bar #
#-----------------------#
min.cut = cutoff
max.cut = max(abs(w))
cutoff.old = cutoff
dev.new("width" = 5, "height" = 2.7, xpos = -1)
def.par = par(no.readonly = TRUE)
cuts = seq(0, 1, length = 21)
par(mai = c(0.25, 0.15, 0.3, 0.15), bg = gray(0.95))
layout(matrix(c(0, 1, 0), ncol = 1, nrow = 3),
widths = 1, heights = c(0.25, 1, 0.25))
plot(cuts, type = "n", rep(0, 21), xlab = "", ylab = "",
xlim = c(-0.10, 1.10), axes = FALSE)
title("cutoff control", cex.main = 1.9, font.main = 1)
text(0.5, -0.6, "value", cex = 1.5)
text(0, -0.6, round(min.cut, 2), cex = 1.4)
text(1, -0.6, round(max.cut, 2), cex = 1.4)
mtext(min.cut, side = 1, line = -1, outer = FALSE, cex = 0.95)
rect(-0.1, -0.3, -0.02, 0.3, col = "white")
rect(1.02, -0.3, 1.1, 0.3, col = "white")
points(1.06, 0, pch = 3, cex = 2.4)
lines(c(-0.085, -0.035), c(0, 0))
for (i in seq(0, 1, length = 21))
lines(c(i, i), c(-0.22, 0.2))
x = pos = 0
rect(-0.01, -0.045, x, 0.04, col = "red")
rect(x, -0.045, 1.01, 0.04, col = "white")
bar.dev = dev.cur()
# construction of the initial graph #
#-----------------------------------#
dev.new()
net.dev = dev.cur()
if (isTRUE(show.color.key))
{
layout(lmat, widths = lwid, heights = lhei, respect = FALSE)
par(mar = c(5, 4, 2, 1), cex = 0.75)
image(z.mat, col = col, xaxt = "n", yaxt = "n")
box()
par(usr = c(0, 1, 0, 1))
axis(1, at = xv, labels = lv, cex.axis = keysize.label)
title("Color key", font.main = 1, cex.main = keysize.label)
par(def.par)
par(new = TRUE)
}
par(pty = "s", mar = c(0, 0, 0, 0))
plot(gR, layout = l)
par(def.par)
old.pos = -1
repeat {
dev.set(bar.dev)
z = locator(1, type = "n")
x = z[[1]]
y = z[[2]]
if (is.null(z)) break
if (0 <= x & x <= 1 & -0.22 <= y & y <= 0.22)
{
rect(0, -0.045, x, 0.04, col = "red")
rect(x, -0.045, 1.01, 0.04, col = "white")
pos = x
}
if (1.02 <= x & x <= 1.1 & -0.3 <= y & y <= 0.3)
{
x = pos + 0.05
idx = which.min(abs(cuts - x))
x = cuts[idx]
pos = x
rect(0, -0.045, x, 0.04, col = "red")
rect(x, -0.045, 1.01, 0.04, col = "white")
}
if (-0.1 <= x & x <= -0.02 & -0.3 <= y & y <= 0.3)
{
x = pos - 0.05
idx = which.min(abs(cuts - x))
x = cuts[idx]
pos = x
rect(0, -0.045, x, 0.04, col = "red")
rect(x, -0.045, 1.01, 0.04, col = "white")
}
if (old.pos != pos)
{
old.pos = pos
rect(0.4, -0.8, 0.6, -1.5, col = gray(0.95), border = NA)
cutoff = (max.cut - min.cut) * pos + min.cut
mtext(round(cutoff, 3), side = 1, line = -1, cex = 0.9)
# new graph plot #
#----------------#
dev.set(net.dev)
if (cutoff >= cutoff.old)
{
# selection of the edges to remove of the network #
#-------------------------------------------------#
supp.edge = E(gR)[abs(E(gR)$weight) < cutoff]
# Generation of the graph with all the significant edges #
#--------------------------------------------------------#
gE = delete.edges(gR, supp.edge)
gE = delete.vertices(gE, which(degree(gE) == 0))
# graph plot #
#------------#
nn = vcount(gE)
V(gR)$label.cex = min(2.5 * cex.node.name/log(nn), 1)
E(gR)$label.cex = min(2.25 * cex.edge.label/log(nn), 1)
cex0 = 2 * V(gE)$label.cex
def.par = par(no.readonly = TRUE)
par(pty = "s", mar = c(0, 0, 0, 0))
plot(1:100, 1:100, type = "n", xaxt = "n")
cha = V(gE)$label
cha = paste("", cha, "")
xh = strwidth(cha, cex = cex0) * 1.5
yh = strheight(cha, cex = cex0) * 3
V(gE)$size = xh
V(gE)$size2 = yh
par(def.par)
if (is.null(layout.fun))
{
l = layout.fruchterman.reingold(gE, weights = (1 - abs(E(gE)$weight)))
} else {
l = layout.fun(gE)
}
if (isTRUE(show.color.key))
{
layout(lmat, widths = lwid, heights = lhei, respect = FALSE)
par(mar = c(5, 4, 2, 1), cex = 0.75)
image(z.mat, col = col, xaxt = "n", yaxt = "n")
box()
par(usr = c(0, 1, 0, 1))
axis(1, at = xv, labels = lv, cex.axis = keysize.label)
title("Color key", font.main = 1, cex.main = keysize.label)
par(def.par)
par(new = TRUE)
}
par(pty = "s", mar = c(0, 0, 0, 0))
plot(gE, layout = l)
par(def.par)
cutoff.old = cutoff
} else {
# selection of the edges to incluir in the network #
#--------------------------------------------------#
supp.edge = E(gR)[abs(E(gR)$weight) < cutoff]
# generation of the graph with all the significant edges #
#--------------------------------------------------------#
gE = delete.edges(gR, supp.edge)
gE = delete.vertices(gE, which(degree(gE) == 0))
# graph plot #
#------------#
nn = vcount(gE)
V(gR)$label.cex = min(2.5 * cex.node.name/log(nn), 1)
E(gR)$label.cex = min(2.25 * cex.edge.label/log(nn), 1)
cex0 = 2 * V(gE)$label.cex
def.par = par(no.readonly = TRUE)
par(pty = "s", mar = c(0, 0, 0, 0))
plot(1:100, 1:100, type = "n", xaxt = "n")
cha = V(gE)$label
cha = paste("", cha, "")
xh = strwidth(cha, cex = cex0) * 1.5
yh = strheight(cha, cex = cex0) * 3
V(gE)$size = xh
V(gE)$size2 = yh
par(def.par)
if (is.null(layout.fun))
{
l = layout.fruchterman.reingold(gE, weights = (1 - abs(E(gE)$weight)))
} else {
l = layout.fun(gE)
}
if (isTRUE(show.color.key))
{
layout(lmat, widths = lwid, heights = lhei, respect = FALSE)
par(mar = c(5, 4, 2, 1), cex = 0.75)
image(z.mat, col = col, xaxt = "n", yaxt = "n")
box()
par(usr = c(0, 1, 0, 1))
axis(1, at = xv, labels = lv, cex.axis = keysize.label)
title("Color key", font.main = 1, cex.main = keysize.label)
par(def.par)
par(new = TRUE)
}
par(pty = "s", mar = c(0, 0, 0, 0))
plot(gE, layout = l)
par(def.par)
cutoff.old = cutoff
}
gE.none = TRUE
}
} # end loop
if (gE.none != FALSE)
gR = gE
}
res=list(gR = gR)
if(any(class.object %in% object.blocks))
{
l = 1
for (i in 1:(length(blocks)-1))
{
for (j in (i + 1):length(blocks))
{
M_block[[l]][abs(M_block[[l]]) < cutoff] = 0
res[paste("M",blocks[i],blocks[j],sep="_")] = list(M_block[[l]])
l = l + 1
}
}
} else {
mat[abs(mat) < cutoff] = 0
res$M=mat
}
res$cutoff = cutoff
if (!is.null(save))
dev.off()
return(invisible(res))
}
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