# R/get_network_colors.R In anipaths: Animation of Multiple Trajectories with Uncertainty

#### Documented in get_network_colorsnetwork_interp

```#' Synchronous interpolation of network using piece-wise constant interpolation
#'
#' @param network array of network observations of dimension (\code{n.indiv, n.indiv, length(network.times)})
#' @param network.times vector of times at which network observations are made
#' @param time.grid times at which network will be interpolated
#'
#' @return array of dimension \code{n.indiv, n.indiv, length(time.grid))}
network_interp <- function(network = NULL, network.times, time.grid){
if(is.null(network)) return(NULL)
time.grid.network <- time.grid[time.grid >= min(network.times) & time.grid <= max(network.times)]
network.interp <- apply(network, 1:2, function(w_ij){
network.interp.ij <- rep(NA, length(time.grid))
network.interp.ij[time.grid %in% time.grid.network] <-
approx(
x = network.times, y = w_ij,
xout = as.numeric(time.grid.network), method = "constant"
)\$y
return(network.interp.ij)
})
return(aperm(network.interp, c(2, 3, 1)))
}

#' get_network_colors()
#' Finds all maximal cliques in the network at each time point and tries to assign them a useful coloring
#' @keywords internal
#'
#' @param binary.network a 3D array giving the time-varying adjecency matrix of a dynamic network.
#' @param network.color.options vector of colors
#'
#' @return a list of two elements: a list of the maximal cliques at each time, and c list with colors for each clique at each time
#' @importFrom RColorBrewer brewer.pal
#'
get_network_colors <- function(binary.network, network.color.options = NULL) {

## unique cliques ----
cliques <- sapply(1:dim(binary.network)[3], function(t) {
mode = "undirected",
diag = F
), min = 2), sort))
},
simplify = F
)
unique.cliques <- NULL
clique.lengths <- unlist(lapply(cliques, length))
for (t in (1:dim(binary.network)[3])[which(clique.lengths > 0)]) {
unique.cliques <- unique(c(unique.cliques, cliques[[t]]))
}
if (is.null(network.color.options)) {
network.color.options <- unique(c(
brewer.pal(8, "Dark2"),
brewer.pal(9, "GnBu")[3:9],
brewer.pal(9, "OrRd")[3:9],
brewer.pal(9, "BuPu")[3:9],
brewer.pal(9, "YlGn")[3:9],
brewer.pal(9, "PuBu")[3:9],
brewer.pal(9, "YlOrBr")[3:9],
brewer.pal(9, "YlGnBu")[3:9],
brewer.pal(9, "PuRd")[3:9],
brewer.pal(9, "PuBuGn")[3:9],
brewer.pal(9, "Purples")[3:9],
brewer.pal(9, "Oranges")[3:9]
))
}
if (length(unique.cliques) > length(network.color.options)) {
network.color.options <- c(
network.color.options,
rep("wheat4", length(unique.cliques) - length(network.color.options))
)
}
available.colors <- network.color.options
clique.colors <- vector("list", dim(binary.network)[3])

## paint network ----
for (t in (1:dim(binary.network)[3])) {
if (t == 1) {
clique.colors[[t]] <- rep("black", length(cliques[[t]]))
for (c in 1:length(cliques[[t]])) {
clique.colors[[1]][c] <- available.colors[1]
available.colors <- available.colors[-1]
}
} else {
if (clique.lengths[t] == 0) {
cliques[[t]] <- NA
clique.colors[[t]] <- NA
next
}
available.colors <- available.colors[!(available.colors %in% clique.colors[[t - 1]])]
clique.colors[[t]] <- rep("black", length(cliques[[t]]))
for (c in 1:length(cliques[[t]])) {
from.b4 <- lapply(cliques[[t - 1]], function(c.tm1) {
intersect(as.numeric(c.tm1), as.numeric(cliques[[t]][[c]]))
})

## (1) check to see if this clique is nested inside a previous one ----
nested.b4 <- which(unlist(lapply(from.b4, function(intersection) {
identical(as.numeric(intersection), as.numeric(cliques[[t]][[c]]))
})))
nested.b4 <- nested.b4[which(!(clique.colors[[t - 1]][nested.b4] %in% clique.colors[[t]]))]
if (length(nested.b4) > 0) {
clique.colors[[t]][c] <- clique.colors[[t - 1]][min(nested.b4)]
} else {

## (2) check to see if a previous clique is nested inside this one ----
rev.nested.b4 <- which(sapply(1:length(from.b4), function(cl) {
identical(as.numeric(from.b4[[cl]]), as.numeric(cliques[[t - 1]][[cl]]))
}))
rev.nested.b4 <- rev.nested.b4[which(!(clique.colors[[t - 1]][rev.nested.b4] %in% clique.colors[[t]]))]
if (length(rev.nested.b4) > 0) {
clique.colors[[t]][c] <- clique.colors[[t - 1]][min(rev.nested.b4)]
} else {

## laste resort: add a new color ----
if (!is.na(available.colors[1])) {
clique.colors[[t]][c] <- available.colors[1]
available.colors <- available.colors[-1]
} else {

## if I ran out of colors, use network.color.options[1]
clique.colors[[t]][c] <- network.color.options[1]
}
}
}
}
}
}
return(list("colors" = clique.colors, "cliques" = cliques))
}
```

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anipaths documentation built on May 17, 2021, 5:07 p.m.