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R/plot.select.R
In BGGM: Bayesian Gaussian Graphical Models
Defines functions
plot.select
Documented in
plot.select
#' Network Plot for \code{select} Objects
#'
#' Visualize the conditional (in)dependence structure.
#'
#' @param x An object of class \code{select}.
#'
#' @param layout Character string. Which graph layout (defaults is \code{circle}) ?
#' See \link[sna]{gplot.layout}.
#'
#' @param pos_col Character string. Color for the positive edges (defaults to \code{green}).
#'
#' @param neg_col Character string. Color for the negative edges (defaults to \code{green}).
#'
#' @param node_size Numeric. The size of the nodes (defaults to \code{10}).
#'
#' @param edge_magnify Numeric. A value that is multiplied by the edge weights. This increases (> 1) or
#' decrease (< 1) the line widths (defaults to 1).
#'
#' @param groups A character string of length \emph{p} (the number of nodes in the model).
#' This indicates groups of nodes that should be the same color
#' (e.g., "clusters" or "communities").
#'
#' @param palette A character string sepcifying the palette for the \code{groups}.
#' (default is \code{Set3}). See \href{http://www.cookbook-r.com/Graphs/Colors_(ggplot2)/}{palette options here}.
#'
#' @param ... Additional options passed to \link[GGally]{ggnet2}
#'
#' @importFrom GGally ggnet2
#'
#' @importFrom network network.vertex.names<- set.edge.value set.edge.attribute %e% %v%<- network
#'
#' @importFrom sna gplot.layout.circle
#'
#' @return An object (or list of objects) of class \code{ggplot}
#' that can then be further customized.
#'
#' @note
#' A more extensive example of a custom plot is
#' provided \href{https://donaldrwilliams.github.io/BGGM/articles/netplot.html}{here}
#'
#' @examples
#' \donttest{
#' #########################
#' ### example 1: one ggm ##
#' #########################
#'
#' # data
#' Y <- bfi[,1:25]
#'
#' # estimate
#' fit <- estimate(Y, iter = 250,
#' progress = FALSE)
#'
#' # "communities"
#' comm <- substring(colnames(Y), 1, 1)
#'
#' # edge set
#' E <- select(fit)
#'
#' # plot edge set
#' plt_E <- plot(E, edge_magnify = 5,
#' palette = "Set1",
#' groups = comm)
#'
#'
#' #############################
#' ### example 2: ggm compare ##
#' #############################
#' # compare males vs. females
#'
#' # data
#' Y <- bfi[,1:26]
#'
#' Ym <- subset(Y, gender == 1,
#' select = -gender)
#'
#' Yf <- subset(Y, gender == 2,
#' select = -gender)
#'
#' # estimate
#' fit <- ggm_compare_estimate(Ym, Yf, iter = 250,
#' progress = FALSE)
#'
#' # "communities"
#' comm <- substring(colnames(Ym), 1, 1)
#'
#' # edge set
#' E <- select(fit)
#'
#' # plot edge set
#' plt_E <- plot(E, edge_magnify = 5,
#' palette = "Set1",
#' groups = comm)
#'
#'
#'}
#'
#' @export
plot.select <- function(x,
layout = "circle",
pos_col = "#009E73",
neg_col = "#D55E00",
node_size = 10,
edge_magnify = 1,
groups = NULL,
palette = "Set3",
...){
# select estimate
if(is(x, "select.estimate")){
cn <- colnames(x$object$Y)
p <- ncol(x$pcor_adj)
diag(x$pcor_adj) <- 0
net <- network::network(x$pcor_adj)
if(is.null(cn) ) {
cn <- 1:p
}
# edge weights
network::set.edge.value(x = net, attrname = "weights",
value = x$pcor_adj)
# edge weights absolute
network::set.edge.value(x = net, attrname = "abs_weights",
value = abs(x$pcor_adj) * edge_magnify)
# edge colors
network::set.edge.attribute(x = net, attrname = "edge_color",
value = ifelse(net %e% "weights" < 0,
neg_col,
pos_col))
e <- abs(as.numeric(x$pcor_adj))
if(is.null(groups)){
plt <- ggnet2(net, edge.alpha = e[e != 0] / max(e),
edge.size = "abs_weights",
edge.color = "edge_color",
node.size = 1,
mode = layout, ...) +
geom_point(color = "black",
size = node_size+1) +
geom_point(size = node_size, color = "white") +
guides(color = FALSE) +
geom_text(label = cn)
} else {
net %v% "group" <- groups
suppressMessages(
plt <- ggnet2(net, edge.alpha = e[e != 0] / max(e),
edge.size = "abs_weights",
edge.color = "edge_color",
node.color = "group",
node.size = 1,
mode = layout,
...) +
geom_point(aes(color = groups),
size = node_size + 2,
alpha = 0.2) +
geom_point(aes(color = groups),
size = node_size,
alpha = 1) +
guides(colour = guide_legend(override.aes = list(size=node_size))) +
theme(legend.title = element_blank()) +
scale_color_brewer(palette = palette) +
geom_text(label = cn)
)
}
list(plt = plt)
# end: select.estimate
} else if (is(x, "select.explore")){
if(x$alternative == "two.sided" |
x$alternative == "greater" |
x$alternative == "less"){
cn <- colnames(x$object$Y)
p <- ncol(x$pcor_mat_zero)
diag(x$pcor_mat_zero) <- 0
if(x$alternative == "two.sided"){
Adj_alt <- x$Adj_10
Adj_null <- x$Adj_01
}
if(x$alternative == "greater" |
x$alternative == "less"){
warning(paste0("interpret the conditional indepedence structure cautiously, as the Bayes factor\n",
"is a measure of 'relative' evidence. In this case, ",
x$alternative, " than zero was compared\n",
"to a null model. This does not consider the opposite direction."
))
Adj_alt <- x$Adj_20
Adj_null <- x$Adj_02
}
ambiguous <- matrix(1, p, p) - diag(p) - Adj_alt - Adj_null
net_alt <- network::network(x$pcor_mat_zero)
net_null <- network::network(Adj_null)
net_ambigous <- network::network(ambiguous)
if(is.null(cn) ) {
cn <- 1:p
}
# edge weights
network::set.edge.value(x = net_alt, attrname = "weights",
value = x$pcor_mat_zero)
# edge weights absolute
network::set.edge.value(x = net_alt, attrname = "abs_weights",
value = abs(x$pcor_mat_zero) * edge_magnify)
# edge colors
network::set.edge.attribute(x = net_alt, attrname = "edge_color",
value = ifelse(net_alt %e% "weights" < 0,
neg_col,
pos_col))
e <- abs(as.numeric( x$pcor_mat_zero))
if(is.null(groups)){
plt_alt <- ggnet2(
net_alt,
edge.alpha = e[e != 0] / max(e),
edge.size = "abs_weights",
edge.color = "edge_color",
node.size = 1,
mode = layout
) +
geom_point(color = "black",
size = node_size + 1) +
geom_point(size = node_size, color = "white") +
guides(color = FALSE) +
geom_text(label = cn)
plt_null <- ggnet2(net_null,
node.size = 1,
mode = layout) +
geom_point(color = "black",
size = node_size + 1) +
geom_point(size = node_size, color = "white") +
guides(color = FALSE) +
geom_text(label = cn)
plt_ambiguous <- ggnet2(net_ambigous,
node.size = 1,
mode = layout) +
geom_point(color = "black",
size = node_size + 1) +
geom_point(size = node_size, color = "white") +
guides(color = FALSE) +
geom_text(label = cn)
list(plt_alt = plt_alt,
plt_null = plt_null,
plt_ambiguous = plt_ambiguous)
} else {
net_alt %v% "group" <- groups
net_null %v% "group" <- groups
net_ambigous %v% "group" <- groups
suppressMessages(
plt_alt <- ggnet2(net_alt, edge.alpha = e[e != 0] / max(e),
edge.size = "abs_weights",
edge.color = "edge_color",
node.color = "group",
node.size = 1,
mode = layout) +
geom_point(aes(color = groups),
size = node_size + 2,
alpha = 0.2) +
geom_point(aes(color = groups),
size = node_size,
alpha = 1) +
guides(colour = guide_legend(override.aes = list(size=node_size))) +
theme(legend.title = element_blank()) +
scale_color_brewer(palette = palette) +
geom_text(label = cn)
)
suppressMessages(
plt_null <- ggnet2(net_null,
node.size = 1,
node.color = "group",
mode = layout) +
geom_point(aes(color = groups),
size = node_size + 2,
alpha = 0.2) +
geom_point(aes(color = groups),
size = node_size,
alpha = 1) +
guides(colour = guide_legend(override.aes = list(size=node_size))) +
theme(legend.title = element_blank()) +
scale_color_brewer(palette = palette) +
geom_text(label = cn)
)
suppressMessages(
plt_ambiguous <- ggnet2(net_ambigous,
node.size = 1,
node.color = "group",
mode = layout) +
geom_point(aes(color = groups),
size = node_size + 2,
alpha = 0.2) +
geom_point(aes(color = groups),
size = node_size,
alpha = 1) +
guides(colour = guide_legend(override.aes = list(size=node_size))) +
theme(legend.title = element_blank()) +
scale_color_brewer(palette = palette) +
geom_text(label = cn)
)
list(H1_plt = plt_alt,
H0_plt = plt_null,
ambiguous_plt = plt_ambiguous)
} # end groups
} else if(x$alternative == "exhaustive"){
cn <- colnames(x$object$Y)
p <- ncol(x$pcor_mat)
diag(x$pcor_mat) <- 0
ambiguous <- ifelse((x$neg_mat + x$pos_mat + x$null_mat) == 0, 1, 0)
net_pos <- network::network(x$pos_mat * x$pcor_mat)
net_neg <- network::network(x$neg_mat * x$pcor_mat)
net_null <- network::network(x$null_mat)
net_ambigous <- network::network(ambiguous)
if(is.null(cn) ) {
cn <- 1:p
}
# positive
# edge weights
network::set.edge.value(x = net_pos, attrname = "weights",
value = x$pos_mat * x$pcor_mat)
# edge weights absolute
network::set.edge.value(x = net_pos, attrname = "abs_weights",
value = abs(x$pos_mat * x$pcor_mat) * edge_magnify)
# edge colors
network::set.edge.attribute(x = net_pos, attrname = "edge_color",
value = ifelse(net_pos %e% "weights" < 0,
neg_col,
pos_col))
# negative
# edge weights
network::set.edge.value(x = net_neg, attrname = "weights",
value = x$neg_mat * x$pcor_mat)
# edge weights absolute
network::set.edge.value(x = net_neg, attrname = "abs_weights",
value = abs(x$neg_mat * x$pcor_mat ) * edge_magnify)
# edge colors
network::set.edge.attribute(x = net_neg, attrname = "edge_color",
value = ifelse(net_neg %e% "weights" < 0,
neg_col,
pos_col))
if(is.null(groups)){
e <- abs(as.numeric( x$pcor_mat * x$pos_mat))
plt_pos <- ggnet2(
net_pos,
edge.alpha = e[e != 0] / max(e),
edge.size = "abs_weights",
edge.color = "edge_color",
node.size = 1,
mode = layout
) +
geom_point(color = "black",
size = node_size + 1) +
geom_point(size = node_size, color = "white") +
guides(color = FALSE) +
geom_text(label = cn)
e <- abs(as.numeric( x$pcor_mat * x$neg_mat))
plt_neg <- ggnet2(net_neg,
node.size = 1,
edge.alpha = e[e != 0] / max(e),
edge.size = "abs_weights",
edge.color = "edge_color",
mode = layout) +
geom_point(color = "black",
size = node_size + 1) +
geom_point(size = node_size, color = "white") +
guides(color = FALSE) +
geom_text(label = cn)
plt_null <- ggnet2(net_null,
node.size = 1,
mode = layout) +
geom_point(color = "black",
size = node_size + 1) +
geom_point(size = node_size, color = "white") +
guides(color = FALSE) +
geom_text(label = cn)
plt_ambiguous <- ggnet2(net_ambigous,
node.size = 1,
mode = layout) +
geom_point(color = "black",
size = node_size + 1) +
geom_point(size = node_size, color = "white") +
guides(color = FALSE) +
geom_text(label = cn)
list(plt_pos = plt_pos,
plt_neg = plt_neg,
plt_null = plt_null,
plt_ambiguous = plt_ambiguous)
} else {
net_pos %v% "group" <- groups
net_neg %v% "group" <- groups
net_null %v% "group" <- groups
net_ambigous %v% "group" <- groups
e <- abs(as.numeric( x$pcor_mat * x$pos_mat))
suppressMessages(
plt_pos <- ggnet2(
net_pos,
edge.alpha = e[e != 0] / max(e),
edge.size = "abs_weights",
edge.color = "edge_color",
node.size = 1,
node.color = "group",
mode = layout
) +
geom_point(aes(color = groups),
size = node_size + 2,
alpha = 0.2) +
geom_point(aes(color = groups),
size = node_size,
alpha = 1) +
guides(colour = guide_legend(override.aes = list(size=node_size))) +
theme(legend.title = element_blank()) +
scale_color_brewer(palette = palette) +
geom_text(label = cn)
)
e <- abs(as.numeric( x$pcor_mat * x$neg_mat))
suppressMessages(
plt_neg <- ggnet2(net_neg,
node.size = 1,
edge.alpha = e[e != 0] / max(e),
edge.size = "abs_weights",
edge.color = "edge_color",
node.color = "group",
mode = layout) +
geom_point(aes(color = groups),
size = node_size + 2,
alpha = 0.2) +
geom_point(aes(color = groups),
size = node_size,
alpha = 1) +
guides(colour = guide_legend(override.aes = list(size=node_size))) +
theme(legend.title = element_blank()) +
scale_color_brewer(palette = palette) +
geom_text(label = cn)
)
suppressMessages(
plt_null <- ggnet2(net_null,
node.size = 1,
mode = layout,
node.color = "group") +
geom_point(aes(color = groups),
size = node_size + 2,
alpha = 0.2) +
geom_point(aes(color = groups),
size = node_size,
alpha = 1) +
guides(colour = guide_legend(override.aes = list(size=node_size))) +
theme(legend.title = element_blank()) +
scale_color_brewer(palette = palette) +
geom_text(label = cn)
)
suppressMessages(
plt_ambiguous <- ggnet2(net_ambigous,
node.size = 1,
mode = layout,
node.color = "group") +
geom_point(aes(color = groups),
size = node_size,
alpha = 1) +
guides(colour = guide_legend(override.aes = list(size=node_size))) +
theme(legend.title = element_blank()) +
scale_color_brewer(palette = palette) +
geom_text(label = cn)
)
list(plt_pos = plt_pos,
plt_neg = plt_neg,
plt_null = plt_null,
plt_ambiguous = plt_ambiguous)
} # end groups
}
} else if(is(x, "select.ggm_compare_estimate")){
cn <- colnames(x$object$info$dat[[1]])
p <- ncol(x$pcor_adj[[1]])
comparisons <- length(x$pcor_adj)
if(is.null(cn) ) {
cn <- 1:p
}
lapply(1:comparisons, function(z){
net <- network::network(x$pcor_adj[[z]])
# edge weights
network::set.edge.value(x = net, attrname = "weights",
value = x$pcor_adj[[z]])
# edge weights absolute
network::set.edge.value(x = net, attrname = "abs_weights",
value = abs(x$pcor_adj[[z]]) * edge_magnify)
# edge colors
network::set.edge.attribute(x = net, attrname = "edge_color",
value = ifelse(net %e% "weights" < 0,
neg_col,
pos_col))
diag(x$pcor_adj[[z]]) <- 0
e <- abs(as.numeric(x$pcor_adj[[z]]))
if(is.null(groups)){
ggnet2(net, edge.alpha = e[e != 0] / max(e),
edge.size = "abs_weights",
edge.color = "edge_color",
node.size = 1,
mode = layout) +
geom_point(color = "black",
size = node_size+1) +
geom_point(size = node_size, color = "white") +
guides(color = FALSE) +
geom_text(label = cn) +
ggtitle(names(x$object$diff)[z])
} else {
net %v% "group" <- groups
suppressMessages(
ggnet2(net, edge.alpha = e[e != 0] / max(e),
edge.size = "abs_weights",
edge.color = "edge_color",
node.color = "group",
node.size = 1,
mode = layout) +
geom_point(aes(color = groups),
size = node_size + 2,
alpha = 0.2) +
geom_point(aes(color = groups),
size = node_size,
alpha = 1) +
guides(colour = guide_legend(override.aes = list(size=node_size))) +
theme(legend.title = element_blank()) +
scale_color_brewer(palette = palette) +
geom_text(label = cn) +
ggtitle(names(x$object$diff[z]))
)
}
})
} else if(is(x, "select.ggm_compare_bf")){
if(x$post_prob == 0.50){
cn <- colnames(x$object$info$dat[[1]])
p <- ncol(x$pcor_adj[[1]])
if(is.null(cn) ){
cn <- 1:p
}
if(length(x$info$dat) == 2){
net_alt <- network::network(x$adj_10 * x$pcor_mat)
net_null <- network::network(x$adj_01)
# edge weights
network::set.edge.value(x = net_alt, attrname = "weights",
value = x$adj_10 * x$pcor_mat)
# edge weights absolute
network::set.edge.value(x = net_alt, attrname = "abs_weights",
value = abs(x$adj_10 * x$pcor_mat) * edge_magnify)
# edge colors
network::set.edge.attribute(x = net_alt, attrname = "edge_color",
value = ifelse(net_alt %e% "weights" < 0,
neg_col,
pos_col))
if(is.null(groups)){
e <- abs(as.numeric( x$pcor_mat * x$adj_10))
plt_alt <- ggnet2(
net_alt,
edge.alpha = e[e != 0] / max(e),
edge.size = "abs_weights",
edge.color = "edge_color",
node.size = 1,
mode = layout,...
) +
geom_point(color = "black",
size = node_size + 1) +
geom_point(size = node_size, color = "white") +
guides(color = FALSE) +
geom_text(label = cn)
plt_null <- ggnet2(net_null,
node.size = 1,
mode = layout) +
geom_point(color = "black",
size = node_size + 1) +
geom_point(size = node_size, color = "white") +
guides(color = FALSE) +
geom_text(label = cn)
list(plt_alt = plt_alt,
plt_null = plt_null)
} else {
net_alt %v% "group" <- groups
net_null %v% "group" <- groups
e <- abs(as.numeric( x$pcor_mat * x$adj_10))
suppressMessages(
plt_alt <- ggnet2(
net_alt,
edge.alpha = e[e != 0] / max(e),
edge.size = "abs_weights",
edge.color = "edge_color",
node.color = "group",
node.size = 1,
mode = layout
) +
geom_point(aes(color = groups),
size = node_size + 2,
alpha = 0.2) +
geom_point(aes(color = groups),
size = node_size,
alpha = 1) +
guides(colour = guide_legend(override.aes = list(size=node_size))) +
theme(legend.title = element_blank()) +
scale_color_brewer(palette = palette) +
geom_text(label = cn)
)
suppressMessages(
plt_null <- ggnet2(net_null,
node.size = 1,
mode = layout,
node.color = "group") +
geom_point(color = "black",
size = node_size + 1) +
geom_point(size = node_size, color = "white") +
guides(color = FALSE) +
geom_text(label = cn) +
geom_point(aes(color = groups),
size = node_size + 2,
alpha = 0.2) +
geom_point(aes(color = groups),
size = node_size,
alpha = 1) +
guides(colour = guide_legend(override.aes = list(size=node_size))) +
theme(legend.title = element_blank()) +
scale_color_brewer(palette = palette) +
geom_text(label = cn)
)
list(plt_alt = plt_alt,
plt_null = plt_null)
} # end clusters
} else {
net_alt <- network::network(x$adj_10)
net_null <- network::network(x$adj_01)
if(is.null(groups)){
plt_alt <- ggnet2(net_alt,
node.size = 1,
mode = layout) +
geom_point(color = "black",
size = node_size + 1) +
geom_point(size = node_size, color = "white") +
guides(color = FALSE) +
geom_text(label = cn)
plt_null <- ggnet2(net_null,
node.size = 1,
mode = layout) +
geom_point(color = "black",
size = node_size + 1) +
geom_point(size = node_size, color = "white") +
guides(color = FALSE) +
geom_text(label = cn)
list(plt_alt = plt_alt,
plt_null = plt_null)
} else {
net_alt %v% "group" <- groups
net_null %v% "group" <- groups
suppressMessages(
plt_alt <- ggnet2(net_alt,
node.size = 1,
mode = layout,
node.color = "group") +
geom_point(color = "black",
size = node_size + 1) +
geom_point(size = node_size, color = "white") +
guides(color = FALSE) +
geom_text(label = cn) +
geom_point(aes(color = groups),
size = node_size + 2,
alpha = 0.2) +
geom_point(aes(color = groups),
size = node_size,
alpha = 1) +
guides(colour = guide_legend(override.aes = list(size=node_size))) +
theme(legend.title = element_blank()) +
scale_color_brewer(palette = palette) +
geom_text(label = cn)
)
suppressMessages(
plt_null <- ggnet2(net_null,
node.size = 1,
mode = layout,
node.color = "group") +
geom_point(color = "black",
size = node_size + 1) +
geom_point(size = node_size, color = "white") +
guides(color = FALSE) +
geom_text(label = cn) +
geom_point(aes(color = groups),
size = node_size + 2,
alpha = 0.2) +
geom_point(aes(color = groups),
size = node_size,
alpha = 1) +
guides(colour = guide_legend(override.aes = list(size=node_size))) +
theme(legend.title = element_blank()) +
scale_color_brewer(palette = palette) +
geom_text(label = cn)
)
list(plt_alt = plt_alt,
plt_null = plt_null)
} # end of clusters
} # end two groups
# more than 0.50
} else {
cn <- colnames(x$object$info$dat[[1]])
p <- ncol(x$BF_10)
if(is.null(cn) ){
cn <- 1:p
}
if(length(x$info$dat) == 2){
Adj_alt <- x$adj_10
Adj_null <- x$adj_01
ambiguous <- matrix(1, p, p) - diag(p) - Adj_alt - Adj_null
net_alt <- network::network(x$pcor_mat_10 * Adj_alt)
net_null <- network::network(Adj_null)
net_ambigous <- network(ambiguous)
# edge weights
network::set.edge.value(x = net_alt, attrname = "weights",
value = x$pcor_mat_10 * Adj_alt)
# edge weights absolute
network::set.edge.value(x = net_alt, attrname = "abs_weights",
value = abs(x$pcor_mat_10 * Adj_alt) * edge_magnify)
# edge colors
network::set.edge.attribute(x = net_alt, attrname = "edge_color",
value = ifelse(net_alt %e% "weights" < 0,
neg_col,
pos_col))
e <- abs(as.numeric( x$pcor_mat_10 * x$adj_10))
if(is.null(groups)){
plt_alt <- ggnet2(
net_alt,
edge.alpha = e[e != 0] / max(e),
edge.size = "abs_weights",
edge.color = "edge_color",
node.size = 1,
mode = layout
) +
geom_point(color = "black",
size = node_size + 1) +
geom_point(size = node_size, color = "white") +
guides(color = FALSE) +
geom_text(label = cn)
plt_null <- ggnet2(net_null,
node.size = 1,
mode = layout) +
geom_point(color = "black",
size = node_size + 1) +
geom_point(size = node_size, color = "white") +
guides(color = FALSE) +
geom_text(label = cn)
plt_ambiguous <- ggnet2(net_ambigous,
node.size = 1,
mode = layout) +
geom_point(color = "black",
size = node_size + 1) +
geom_point(size = node_size, color = "white") +
guides(color = FALSE) +
geom_text(label = cn)
list(plt_alt = plt_alt,
plt_null = plt_null,
plt_ambiguous = plt_ambiguous)
} else {
net_alt %v% "group" <- groups
net_null %v% "group" <- groups
net_ambigous %v% "group" <- groups
suppressMessages(
plt_alt <- ggnet2(net_alt, edge.alpha = e[e != 0] / max(e),
edge.size = "abs_weights",
edge.color = "edge_color",
node.color = "group",
node.size = 1,
mode = layout) +
geom_point(aes(color = groups),
size = node_size + 2,
alpha = 0.2) +
geom_point(aes(color = groups),
size = node_size,
alpha = 1) +
guides(colour = guide_legend(override.aes = list(size=node_size))) +
theme(legend.title = element_blank()) +
scale_color_brewer(palette = palette) +
geom_text(label = cn)
)
suppressMessages(
plt_null <- ggnet2(net_null,
node.size = 1,
node.color = "group",
mode = layout) +
geom_point(aes(color = groups),
size = node_size + 2,
alpha = 0.2) +
geom_point(aes(color = groups),
size = node_size,
alpha = 1) +
guides(colour = guide_legend(override.aes = list(size=node_size))) +
theme(legend.title = element_blank()) +
scale_color_brewer(palette = palette) +
geom_text(label = cn)
)
suppressMessages(
plt_ambiguous <- ggnet2(net_ambigous,
node.size = 1,
node.color = "group",
mode = layout) +
geom_point(aes(color = groups),
size = node_size + 2,
alpha = 0.2) +
geom_point(aes(color = groups),
size = node_size,
alpha = 1) +
guides(colour = guide_legend(override.aes = list(size=node_size))) +
theme(legend.title = element_blank()) +
scale_color_brewer(palette = palette) +
geom_text(label = cn)
)
list(H1_plt = plt_alt,
H0_plt = plt_null,
ambiguous_plt = plt_ambiguous)
} # end cluster
# end: two groups
} else {
Adj_alt <- x$adj_10
Adj_null <- x$adj_01
ambiguous <- matrix(1, p, p) - diag(p) - Adj_alt - Adj_null
net_alt <- network::network(Adj_alt)
net_null <- network::network(Adj_null)
net_ambigous <- network::network(ambiguous)
if(is.null(groups)){
plt_alt <- ggnet2(net_alt,
node.size = 1,
mode = layout) +
geom_point(color = "black",
size = node_size + 1) +
geom_point(size = node_size, color = "white") +
guides(color = FALSE) +
geom_text(label = cn)
plt_null <- ggnet2(net_null,
node.size = 1,
mode = layout) +
geom_point(color = "black",
size = node_size + 1) +
geom_point(size = node_size, color = "white") +
guides(color = FALSE) +
geom_text(label = cn)
plt_ambiguous <- ggnet2(net_ambigous,
node.size = 1,
mode = layout) +
geom_point(color = "black",
size = node_size + 1) +
geom_point(size = node_size, color = "white") +
guides(color = FALSE) +
geom_text(label = cn)
list(plt_alt = plt_alt,
plt_null = plt_null,
plt_ambiguous = plt_ambiguous)
} else {
net_alt %v% "group" <- groups
net_null %v% "group" <- groups
net_ambigous %v% "group" <- groups
suppressMessages(
plt_alt <- ggnet2(net_alt,
node.size = 1,
node.color = "group",
mode = layout) +
geom_point(aes(color = groups),
size = node_size + 2,
alpha = 0.2) +
geom_point(aes(color = groups),
size = node_size,
alpha = 1) +
guides(colour = guide_legend(override.aes = list(size=node_size))) +
theme(legend.title = element_blank()) +
scale_color_brewer(palette = palette) +
geom_text(label = cn)
)
suppressMessages(
plt_null <- ggnet2(net_null,
node.size = 1,
node.color = "group",
mode = layout) +
geom_point(aes(color = groups),
size = node_size + 2,
alpha = 0.2) +
geom_point(aes(color = groups),
size = node_size,
alpha = 1) +
guides(colour = guide_legend(override.aes = list(size=node_size))) +
theme(legend.title = element_blank()) +
scale_color_brewer(palette = palette) +
geom_text(label = cn)
)
suppressMessages(
plt_ambiguous <- ggnet2(net_ambigous,
node.size = 1,
node.color = "group",
mode = layout) +
geom_point(aes(color = groups),
size = node_size + 2,
alpha = 0.2) +
geom_point(aes(color = groups),
size = node_size,
alpha = 1) +
guides(colour = guide_legend(override.aes = list(size=node_size))) +
theme(legend.title = element_blank()) +
scale_color_brewer(palette = palette) +
geom_text(label = cn)
)
list(H1_plt = plt_alt,
H0_plt = plt_null,
ambiguous_plt = plt_ambiguous)
} # end cluster
} # end: more than 2 groups
} # end not 0.50.
} # end select.ggm_compare.explore
else {
stop("object class not currently supported")
}
}
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Defines functions plot.select
Documented in plot.select
#' Network Plot for \code{select} Objects
#'
#' Visualize the conditional (in)dependence structure.
#'
#' @param x An object of class \code{select}.
#'
#' @param layout Character string. Which graph layout (defaults is \code{circle}) ?
#' See \link[sna]{gplot.layout}.
#'
#' @param pos_col Character string. Color for the positive edges (defaults to \code{green}).
#'
#' @param neg_col Character string. Color for the negative edges (defaults to \code{green}).
#'
#' @param node_size Numeric. The size of the nodes (defaults to \code{10}).
#'
#' @param edge_magnify Numeric. A value that is multiplied by the edge weights. This increases (> 1) or
#' decrease (< 1) the line widths (defaults to 1).
#'
#' @param groups A character string of length \emph{p} (the number of nodes in the model).
#' This indicates groups of nodes that should be the same color
#' (e.g., "clusters" or "communities").
#'
#' @param palette A character string sepcifying the palette for the \code{groups}.
#' (default is \code{Set3}). See \href{http://www.cookbook-r.com/Graphs/Colors_(ggplot2)/}{palette options here}.
#'
#' @param ... Additional options passed to \link[GGally]{ggnet2}
#'
#' @importFrom GGally ggnet2
#'
#' @importFrom network network.vertex.names<- set.edge.value set.edge.attribute %e% %v%<- network
#'
#' @importFrom sna gplot.layout.circle
#'
#' @return An object (or list of objects) of class \code{ggplot}
#' that can then be further customized.
#'
#' @note
#' A more extensive example of a custom plot is
#' provided \href{https://donaldrwilliams.github.io/BGGM/articles/netplot.html}{here}
#'
#' @examples
#' \donttest{
#' #########################
#' ### example 1: one ggm ##
#' #########################
#'
#' # data
#' Y <- bfi[,1:25]
#'
#' # estimate
#' fit <- estimate(Y, iter = 250,
#' progress = FALSE)
#'
#' # "communities"
#' comm <- substring(colnames(Y), 1, 1)
#'
#' # edge set
#' E <- select(fit)
#'
#' # plot edge set
#' plt_E <- plot(E, edge_magnify = 5,
#' palette = "Set1",
#' groups = comm)
#'
#'
#' #############################
#' ### example 2: ggm compare ##
#' #############################
#' # compare males vs. females
#'
#' # data
#' Y <- bfi[,1:26]
#'
#' Ym <- subset(Y, gender == 1,
#' select = -gender)
#'
#' Yf <- subset(Y, gender == 2,
#' select = -gender)
#'
#' # estimate
#' fit <- ggm_compare_estimate(Ym, Yf, iter = 250,
#' progress = FALSE)
#'
#' # "communities"
#' comm <- substring(colnames(Ym), 1, 1)
#'
#' # edge set
#' E <- select(fit)
#'
#' # plot edge set
#' plt_E <- plot(E, edge_magnify = 5,
#' palette = "Set1",
#' groups = comm)
#'
#'
#'}
#'
#' @export
plot.select <- function(x,
layout = "circle",
pos_col = "#009E73",
neg_col = "#D55E00",
node_size = 10,
edge_magnify = 1,
groups = NULL,
palette = "Set3",
...){
# select estimate
if(is(x, "select.estimate")){
cn <- colnames(x$object$Y)
p <- ncol(x$pcor_adj)
diag(x$pcor_adj) <- 0
net <- network::network(x$pcor_adj)
if(is.null(cn) ) {
cn <- 1:p
}
# edge weights
network::set.edge.value(x = net, attrname = "weights",
value = x$pcor_adj)
# edge weights absolute
network::set.edge.value(x = net, attrname = "abs_weights",
value = abs(x$pcor_adj) * edge_magnify)
# edge colors
network::set.edge.attribute(x = net, attrname = "edge_color",
value = ifelse(net %e% "weights" < 0,
neg_col,
pos_col))
e <- abs(as.numeric(x$pcor_adj))
if(is.null(groups)){
plt <- ggnet2(net, edge.alpha = e[e != 0] / max(e),
edge.size = "abs_weights",
edge.color = "edge_color",
node.size = 1,
mode = layout, ...) +
geom_point(color = "black",
size = node_size+1) +
geom_point(size = node_size, color = "white") +
guides(color = FALSE) +
geom_text(label = cn)
} else {
net %v% "group" <- groups
suppressMessages(
plt <- ggnet2(net, edge.alpha = e[e != 0] / max(e),
edge.size = "abs_weights",
edge.color = "edge_color",
node.color = "group",
node.size = 1,
mode = layout,
...) +
geom_point(aes(color = groups),
size = node_size + 2,
alpha = 0.2) +
geom_point(aes(color = groups),
size = node_size,
alpha = 1) +
guides(colour = guide_legend(override.aes = list(size=node_size))) +
theme(legend.title = element_blank()) +
scale_color_brewer(palette = palette) +
geom_text(label = cn)
)
}
list(plt = plt)
# end: select.estimate
} else if (is(x, "select.explore")){
if(x$alternative == "two.sided" |
x$alternative == "greater" |
x$alternative == "less"){
cn <- colnames(x$object$Y)
p <- ncol(x$pcor_mat_zero)
diag(x$pcor_mat_zero) <- 0
if(x$alternative == "two.sided"){
Adj_alt <- x$Adj_10
Adj_null <- x$Adj_01
}
if(x$alternative == "greater" |
x$alternative == "less"){
warning(paste0("interpret the conditional indepedence structure cautiously, as the Bayes factor\n",
"is a measure of 'relative' evidence. In this case, ",
x$alternative, " than zero was compared\n",
"to a null model. This does not consider the opposite direction."
))
Adj_alt <- x$Adj_20
Adj_null <- x$Adj_02
}
ambiguous <- matrix(1, p, p) - diag(p) - Adj_alt - Adj_null
net_alt <- network::network(x$pcor_mat_zero)
net_null <- network::network(Adj_null)
net_ambigous <- network::network(ambiguous)
if(is.null(cn) ) {
cn <- 1:p
}
# edge weights
network::set.edge.value(x = net_alt, attrname = "weights",
value = x$pcor_mat_zero)
# edge weights absolute
network::set.edge.value(x = net_alt, attrname = "abs_weights",
value = abs(x$pcor_mat_zero) * edge_magnify)
# edge colors
network::set.edge.attribute(x = net_alt, attrname = "edge_color",
value = ifelse(net_alt %e% "weights" < 0,
neg_col,
pos_col))
e <- abs(as.numeric( x$pcor_mat_zero))
if(is.null(groups)){
plt_alt <- ggnet2(
net_alt,
edge.alpha = e[e != 0] / max(e),
edge.size = "abs_weights",
edge.color = "edge_color",
node.size = 1,
mode = layout
) +
geom_point(color = "black",
size = node_size + 1) +
geom_point(size = node_size, color = "white") +
guides(color = FALSE) +
geom_text(label = cn)
plt_null <- ggnet2(net_null,
node.size = 1,
mode = layout) +
geom_point(color = "black",
size = node_size + 1) +
geom_point(size = node_size, color = "white") +
guides(color = FALSE) +
geom_text(label = cn)
plt_ambiguous <- ggnet2(net_ambigous,
node.size = 1,
mode = layout) +
geom_point(color = "black",
size = node_size + 1) +
geom_point(size = node_size, color = "white") +
guides(color = FALSE) +
geom_text(label = cn)
list(plt_alt = plt_alt,
plt_null = plt_null,
plt_ambiguous = plt_ambiguous)
} else {
net_alt %v% "group" <- groups
net_null %v% "group" <- groups
net_ambigous %v% "group" <- groups
suppressMessages(
plt_alt <- ggnet2(net_alt, edge.alpha = e[e != 0] / max(e),
edge.size = "abs_weights",
edge.color = "edge_color",
node.color = "group",
node.size = 1,
mode = layout) +
geom_point(aes(color = groups),
size = node_size + 2,
alpha = 0.2) +
geom_point(aes(color = groups),
size = node_size,
alpha = 1) +
guides(colour = guide_legend(override.aes = list(size=node_size))) +
theme(legend.title = element_blank()) +
scale_color_brewer(palette = palette) +
geom_text(label = cn)
)
suppressMessages(
plt_null <- ggnet2(net_null,
node.size = 1,
node.color = "group",
mode = layout) +
geom_point(aes(color = groups),
size = node_size + 2,
alpha = 0.2) +
geom_point(aes(color = groups),
size = node_size,
alpha = 1) +
guides(colour = guide_legend(override.aes = list(size=node_size))) +
theme(legend.title = element_blank()) +
scale_color_brewer(palette = palette) +
geom_text(label = cn)
)
suppressMessages(
plt_ambiguous <- ggnet2(net_ambigous,
node.size = 1,
node.color = "group",
mode = layout) +
geom_point(aes(color = groups),
size = node_size + 2,
alpha = 0.2) +
geom_point(aes(color = groups),
size = node_size,
alpha = 1) +
guides(colour = guide_legend(override.aes = list(size=node_size))) +
theme(legend.title = element_blank()) +
scale_color_brewer(palette = palette) +
geom_text(label = cn)
)
list(H1_plt = plt_alt,
H0_plt = plt_null,
ambiguous_plt = plt_ambiguous)
} # end groups
} else if(x$alternative == "exhaustive"){
cn <- colnames(x$object$Y)
p <- ncol(x$pcor_mat)
diag(x$pcor_mat) <- 0
ambiguous <- ifelse((x$neg_mat + x$pos_mat + x$null_mat) == 0, 1, 0)
net_pos <- network::network(x$pos_mat * x$pcor_mat)
net_neg <- network::network(x$neg_mat * x$pcor_mat)
net_null <- network::network(x$null_mat)
net_ambigous <- network::network(ambiguous)
if(is.null(cn) ) {
cn <- 1:p
}
# positive
# edge weights
network::set.edge.value(x = net_pos, attrname = "weights",
value = x$pos_mat * x$pcor_mat)
# edge weights absolute
network::set.edge.value(x = net_pos, attrname = "abs_weights",
value = abs(x$pos_mat * x$pcor_mat) * edge_magnify)
# edge colors
network::set.edge.attribute(x = net_pos, attrname = "edge_color",
value = ifelse(net_pos %e% "weights" < 0,
neg_col,
pos_col))
# negative
# edge weights
network::set.edge.value(x = net_neg, attrname = "weights",
value = x$neg_mat * x$pcor_mat)
# edge weights absolute
network::set.edge.value(x = net_neg, attrname = "abs_weights",
value = abs(x$neg_mat * x$pcor_mat ) * edge_magnify)
# edge colors
network::set.edge.attribute(x = net_neg, attrname = "edge_color",
value = ifelse(net_neg %e% "weights" < 0,
neg_col,
pos_col))
if(is.null(groups)){
e <- abs(as.numeric( x$pcor_mat * x$pos_mat))
plt_pos <- ggnet2(
net_pos,
edge.alpha = e[e != 0] / max(e),
edge.size = "abs_weights",
edge.color = "edge_color",
node.size = 1,
mode = layout
) +
geom_point(color = "black",
size = node_size + 1) +
geom_point(size = node_size, color = "white") +
guides(color = FALSE) +
geom_text(label = cn)
e <- abs(as.numeric( x$pcor_mat * x$neg_mat))
plt_neg <- ggnet2(net_neg,
node.size = 1,
edge.alpha = e[e != 0] / max(e),
edge.size = "abs_weights",
edge.color = "edge_color",
mode = layout) +
geom_point(color = "black",
size = node_size + 1) +
geom_point(size = node_size, color = "white") +
guides(color = FALSE) +
geom_text(label = cn)
plt_null <- ggnet2(net_null,
node.size = 1,
mode = layout) +
geom_point(color = "black",
size = node_size + 1) +
geom_point(size = node_size, color = "white") +
guides(color = FALSE) +
geom_text(label = cn)
plt_ambiguous <- ggnet2(net_ambigous,
node.size = 1,
mode = layout) +
geom_point(color = "black",
size = node_size + 1) +
geom_point(size = node_size, color = "white") +
guides(color = FALSE) +
geom_text(label = cn)
list(plt_pos = plt_pos,
plt_neg = plt_neg,
plt_null = plt_null,
plt_ambiguous = plt_ambiguous)
} else {
net_pos %v% "group" <- groups
net_neg %v% "group" <- groups
net_null %v% "group" <- groups
net_ambigous %v% "group" <- groups
e <- abs(as.numeric( x$pcor_mat * x$pos_mat))
suppressMessages(
plt_pos <- ggnet2(
net_pos,
edge.alpha = e[e != 0] / max(e),
edge.size = "abs_weights",
edge.color = "edge_color",
node.size = 1,
node.color = "group",
mode = layout
) +
geom_point(aes(color = groups),
size = node_size + 2,
alpha = 0.2) +
geom_point(aes(color = groups),
size = node_size,
alpha = 1) +
guides(colour = guide_legend(override.aes = list(size=node_size))) +
theme(legend.title = element_blank()) +
scale_color_brewer(palette = palette) +
geom_text(label = cn)
)
e <- abs(as.numeric( x$pcor_mat * x$neg_mat))
suppressMessages(
plt_neg <- ggnet2(net_neg,
node.size = 1,
edge.alpha = e[e != 0] / max(e),
edge.size = "abs_weights",
edge.color = "edge_color",
node.color = "group",
mode = layout) +
geom_point(aes(color = groups),
size = node_size + 2,
alpha = 0.2) +
geom_point(aes(color = groups),
size = node_size,
alpha = 1) +
guides(colour = guide_legend(override.aes = list(size=node_size))) +
theme(legend.title = element_blank()) +
scale_color_brewer(palette = palette) +
geom_text(label = cn)
)
suppressMessages(
plt_null <- ggnet2(net_null,
node.size = 1,
mode = layout,
node.color = "group") +
geom_point(aes(color = groups),
size = node_size + 2,
alpha = 0.2) +
geom_point(aes(color = groups),
size = node_size,
alpha = 1) +
guides(colour = guide_legend(override.aes = list(size=node_size))) +
theme(legend.title = element_blank()) +
scale_color_brewer(palette = palette) +
geom_text(label = cn)
)
suppressMessages(
plt_ambiguous <- ggnet2(net_ambigous,
node.size = 1,
mode = layout,
node.color = "group") +
geom_point(aes(color = groups),
size = node_size,
alpha = 1) +
guides(colour = guide_legend(override.aes = list(size=node_size))) +
theme(legend.title = element_blank()) +
scale_color_brewer(palette = palette) +
geom_text(label = cn)
)
list(plt_pos = plt_pos,
plt_neg = plt_neg,
plt_null = plt_null,
plt_ambiguous = plt_ambiguous)
} # end groups
}
} else if(is(x, "select.ggm_compare_estimate")){
cn <- colnames(x$object$info$dat[[1]])
p <- ncol(x$pcor_adj[[1]])
comparisons <- length(x$pcor_adj)
if(is.null(cn) ) {
cn <- 1:p
}
lapply(1:comparisons, function(z){
net <- network::network(x$pcor_adj[[z]])
# edge weights
network::set.edge.value(x = net, attrname = "weights",
value = x$pcor_adj[[z]])
# edge weights absolute
network::set.edge.value(x = net, attrname = "abs_weights",
value = abs(x$pcor_adj[[z]]) * edge_magnify)
# edge colors
network::set.edge.attribute(x = net, attrname = "edge_color",
value = ifelse(net %e% "weights" < 0,
neg_col,
pos_col))
diag(x$pcor_adj[[z]]) <- 0
e <- abs(as.numeric(x$pcor_adj[[z]]))
if(is.null(groups)){
ggnet2(net, edge.alpha = e[e != 0] / max(e),
edge.size = "abs_weights",
edge.color = "edge_color",
node.size = 1,
mode = layout) +
geom_point(color = "black",
size = node_size+1) +
geom_point(size = node_size, color = "white") +
guides(color = FALSE) +
geom_text(label = cn) +
ggtitle(names(x$object$diff)[z])
} else {
net %v% "group" <- groups
suppressMessages(
ggnet2(net, edge.alpha = e[e != 0] / max(e),
edge.size = "abs_weights",
edge.color = "edge_color",
node.color = "group",
node.size = 1,
mode = layout) +
geom_point(aes(color = groups),
size = node_size + 2,
alpha = 0.2) +
geom_point(aes(color = groups),
size = node_size,
alpha = 1) +
guides(colour = guide_legend(override.aes = list(size=node_size))) +
theme(legend.title = element_blank()) +
scale_color_brewer(palette = palette) +
geom_text(label = cn) +
ggtitle(names(x$object$diff[z]))
)
}
})
} else if(is(x, "select.ggm_compare_bf")){
if(x$post_prob == 0.50){
cn <- colnames(x$object$info$dat[[1]])
p <- ncol(x$pcor_adj[[1]])
if(is.null(cn) ){
cn <- 1:p
}
if(length(x$info$dat) == 2){
net_alt <- network::network(x$adj_10 * x$pcor_mat)
net_null <- network::network(x$adj_01)
# edge weights
network::set.edge.value(x = net_alt, attrname = "weights",
value = x$adj_10 * x$pcor_mat)
# edge weights absolute
network::set.edge.value(x = net_alt, attrname = "abs_weights",
value = abs(x$adj_10 * x$pcor_mat) * edge_magnify)
# edge colors
network::set.edge.attribute(x = net_alt, attrname = "edge_color",
value = ifelse(net_alt %e% "weights" < 0,
neg_col,
pos_col))
if(is.null(groups)){
e <- abs(as.numeric( x$pcor_mat * x$adj_10))
plt_alt <- ggnet2(
net_alt,
edge.alpha = e[e != 0] / max(e),
edge.size = "abs_weights",
edge.color = "edge_color",
node.size = 1,
mode = layout,...
) +
geom_point(color = "black",
size = node_size + 1) +
geom_point(size = node_size, color = "white") +
guides(color = FALSE) +
geom_text(label = cn)
plt_null <- ggnet2(net_null,
node.size = 1,
mode = layout) +
geom_point(color = "black",
size = node_size + 1) +
geom_point(size = node_size, color = "white") +
guides(color = FALSE) +
geom_text(label = cn)
list(plt_alt = plt_alt,
plt_null = plt_null)
} else {
net_alt %v% "group" <- groups
net_null %v% "group" <- groups
e <- abs(as.numeric( x$pcor_mat * x$adj_10))
suppressMessages(
plt_alt <- ggnet2(
net_alt,
edge.alpha = e[e != 0] / max(e),
edge.size = "abs_weights",
edge.color = "edge_color",
node.color = "group",
node.size = 1,
mode = layout
) +
geom_point(aes(color = groups),
size = node_size + 2,
alpha = 0.2) +
geom_point(aes(color = groups),
size = node_size,
alpha = 1) +
guides(colour = guide_legend(override.aes = list(size=node_size))) +
theme(legend.title = element_blank()) +
scale_color_brewer(palette = palette) +
geom_text(label = cn)
)
suppressMessages(
plt_null <- ggnet2(net_null,
node.size = 1,
mode = layout,
node.color = "group") +
geom_point(color = "black",
size = node_size + 1) +
geom_point(size = node_size, color = "white") +
guides(color = FALSE) +
geom_text(label = cn) +
geom_point(aes(color = groups),
size = node_size + 2,
alpha = 0.2) +
geom_point(aes(color = groups),
size = node_size,
alpha = 1) +
guides(colour = guide_legend(override.aes = list(size=node_size))) +
theme(legend.title = element_blank()) +
scale_color_brewer(palette = palette) +
geom_text(label = cn)
)
list(plt_alt = plt_alt,
plt_null = plt_null)
} # end clusters
} else {
net_alt <- network::network(x$adj_10)
net_null <- network::network(x$adj_01)
if(is.null(groups)){
plt_alt <- ggnet2(net_alt,
node.size = 1,
mode = layout) +
geom_point(color = "black",
size = node_size + 1) +
geom_point(size = node_size, color = "white") +
guides(color = FALSE) +
geom_text(label = cn)
plt_null <- ggnet2(net_null,
node.size = 1,
mode = layout) +
geom_point(color = "black",
size = node_size + 1) +
geom_point(size = node_size, color = "white") +
guides(color = FALSE) +
geom_text(label = cn)
list(plt_alt = plt_alt,
plt_null = plt_null)
} else {
net_alt %v% "group" <- groups
net_null %v% "group" <- groups
suppressMessages(
plt_alt <- ggnet2(net_alt,
node.size = 1,
mode = layout,
node.color = "group") +
geom_point(color = "black",
size = node_size + 1) +
geom_point(size = node_size, color = "white") +
guides(color = FALSE) +
geom_text(label = cn) +
geom_point(aes(color = groups),
size = node_size + 2,
alpha = 0.2) +
geom_point(aes(color = groups),
size = node_size,
alpha = 1) +
guides(colour = guide_legend(override.aes = list(size=node_size))) +
theme(legend.title = element_blank()) +
scale_color_brewer(palette = palette) +
geom_text(label = cn)
)
suppressMessages(
plt_null <- ggnet2(net_null,
node.size = 1,
mode = layout,
node.color = "group") +
geom_point(color = "black",
size = node_size + 1) +
geom_point(size = node_size, color = "white") +
guides(color = FALSE) +
geom_text(label = cn) +
geom_point(aes(color = groups),
size = node_size + 2,
alpha = 0.2) +
geom_point(aes(color = groups),
size = node_size,
alpha = 1) +
guides(colour = guide_legend(override.aes = list(size=node_size))) +
theme(legend.title = element_blank()) +
scale_color_brewer(palette = palette) +
geom_text(label = cn)
)
list(plt_alt = plt_alt,
plt_null = plt_null)
} # end of clusters
} # end two groups
# more than 0.50
} else {
cn <- colnames(x$object$info$dat[[1]])
p <- ncol(x$BF_10)
if(is.null(cn) ){
cn <- 1:p
}
if(length(x$info$dat) == 2){
Adj_alt <- x$adj_10
Adj_null <- x$adj_01
ambiguous <- matrix(1, p, p) - diag(p) - Adj_alt - Adj_null
net_alt <- network::network(x$pcor_mat_10 * Adj_alt)
net_null <- network::network(Adj_null)
net_ambigous <- network(ambiguous)
# edge weights
network::set.edge.value(x = net_alt, attrname = "weights",
value = x$pcor_mat_10 * Adj_alt)
# edge weights absolute
network::set.edge.value(x = net_alt, attrname = "abs_weights",
value = abs(x$pcor_mat_10 * Adj_alt) * edge_magnify)
# edge colors
network::set.edge.attribute(x = net_alt, attrname = "edge_color",
value = ifelse(net_alt %e% "weights" < 0,
neg_col,
pos_col))
e <- abs(as.numeric( x$pcor_mat_10 * x$adj_10))
if(is.null(groups)){
plt_alt <- ggnet2(
net_alt,
edge.alpha = e[e != 0] / max(e),
edge.size = "abs_weights",
edge.color = "edge_color",
node.size = 1,
mode = layout
) +
geom_point(color = "black",
size = node_size + 1) +
geom_point(size = node_size, color = "white") +
guides(color = FALSE) +
geom_text(label = cn)
plt_null <- ggnet2(net_null,
node.size = 1,
mode = layout) +
geom_point(color = "black",
size = node_size + 1) +
geom_point(size = node_size, color = "white") +
guides(color = FALSE) +
geom_text(label = cn)
plt_ambiguous <- ggnet2(net_ambigous,
node.size = 1,
mode = layout) +
geom_point(color = "black",
size = node_size + 1) +
geom_point(size = node_size, color = "white") +
guides(color = FALSE) +
geom_text(label = cn)
list(plt_alt = plt_alt,
plt_null = plt_null,
plt_ambiguous = plt_ambiguous)
} else {
net_alt %v% "group" <- groups
net_null %v% "group" <- groups
net_ambigous %v% "group" <- groups
suppressMessages(
plt_alt <- ggnet2(net_alt, edge.alpha = e[e != 0] / max(e),
edge.size = "abs_weights",
edge.color = "edge_color",
node.color = "group",
node.size = 1,
mode = layout) +
geom_point(aes(color = groups),
size = node_size + 2,
alpha = 0.2) +
geom_point(aes(color = groups),
size = node_size,
alpha = 1) +
guides(colour = guide_legend(override.aes = list(size=node_size))) +
theme(legend.title = element_blank()) +
scale_color_brewer(palette = palette) +
geom_text(label = cn)
)
suppressMessages(
plt_null <- ggnet2(net_null,
node.size = 1,
node.color = "group",
mode = layout) +
geom_point(aes(color = groups),
size = node_size + 2,
alpha = 0.2) +
geom_point(aes(color = groups),
size = node_size,
alpha = 1) +
guides(colour = guide_legend(override.aes = list(size=node_size))) +
theme(legend.title = element_blank()) +
scale_color_brewer(palette = palette) +
geom_text(label = cn)
)
suppressMessages(
plt_ambiguous <- ggnet2(net_ambigous,
node.size = 1,
node.color = "group",
mode = layout) +
geom_point(aes(color = groups),
size = node_size + 2,
alpha = 0.2) +
geom_point(aes(color = groups),
size = node_size,
alpha = 1) +
guides(colour = guide_legend(override.aes = list(size=node_size))) +
theme(legend.title = element_blank()) +
scale_color_brewer(palette = palette) +
geom_text(label = cn)
)
list(H1_plt = plt_alt,
H0_plt = plt_null,
ambiguous_plt = plt_ambiguous)
} # end cluster
# end: two groups
} else {
Adj_alt <- x$adj_10
Adj_null <- x$adj_01
ambiguous <- matrix(1, p, p) - diag(p) - Adj_alt - Adj_null
net_alt <- network::network(Adj_alt)
net_null <- network::network(Adj_null)
net_ambigous <- network::network(ambiguous)
if(is.null(groups)){
plt_alt <- ggnet2(net_alt,
node.size = 1,
mode = layout) +
geom_point(color = "black",
size = node_size + 1) +
geom_point(size = node_size, color = "white") +
guides(color = FALSE) +
geom_text(label = cn)
plt_null <- ggnet2(net_null,
node.size = 1,
mode = layout) +
geom_point(color = "black",
size = node_size + 1) +
geom_point(size = node_size, color = "white") +
guides(color = FALSE) +
geom_text(label = cn)
plt_ambiguous <- ggnet2(net_ambigous,
node.size = 1,
mode = layout) +
geom_point(color = "black",
size = node_size + 1) +
geom_point(size = node_size, color = "white") +
guides(color = FALSE) +
geom_text(label = cn)
list(plt_alt = plt_alt,
plt_null = plt_null,
plt_ambiguous = plt_ambiguous)
} else {
net_alt %v% "group" <- groups
net_null %v% "group" <- groups
net_ambigous %v% "group" <- groups
suppressMessages(
plt_alt <- ggnet2(net_alt,
node.size = 1,
node.color = "group",
mode = layout) +
geom_point(aes(color = groups),
size = node_size + 2,
alpha = 0.2) +
geom_point(aes(color = groups),
size = node_size,
alpha = 1) +
guides(colour = guide_legend(override.aes = list(size=node_size))) +
theme(legend.title = element_blank()) +
scale_color_brewer(palette = palette) +
geom_text(label = cn)
)
suppressMessages(
plt_null <- ggnet2(net_null,
node.size = 1,
node.color = "group",
mode = layout) +
geom_point(aes(color = groups),
size = node_size + 2,
alpha = 0.2) +
geom_point(aes(color = groups),
size = node_size,
alpha = 1) +
guides(colour = guide_legend(override.aes = list(size=node_size))) +
theme(legend.title = element_blank()) +
scale_color_brewer(palette = palette) +
geom_text(label = cn)
)
suppressMessages(
plt_ambiguous <- ggnet2(net_ambigous,
node.size = 1,
node.color = "group",
mode = layout) +
geom_point(aes(color = groups),
size = node_size + 2,
alpha = 0.2) +
geom_point(aes(color = groups),
size = node_size,
alpha = 1) +
guides(colour = guide_legend(override.aes = list(size=node_size))) +
theme(legend.title = element_blank()) +
scale_color_brewer(palette = palette) +
geom_text(label = cn)
)
list(H1_plt = plt_alt,
H0_plt = plt_null,
ambiguous_plt = plt_ambiguous)
} # end cluster
} # end: more than 2 groups
} # end not 0.50.
} # end select.ggm_compare.explore
else {
stop("object class not currently supported")
}
}
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