72 lines
2.2 KiB
R
72 lines
2.2 KiB
R
generate_overview_graph <- function() {
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sealKey()
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scCCnet <- readRDS("./data/scCCnet.rds") # S. cerevisiae Cell Cycle network
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scCCnet_ns <- scCCnet[-3] # Remove scores
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graph <- igraph::graph_from_edgelist(as.matrix(scCCnet_ns), directed = FALSE)
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degrees <- igraph::degree(graph, normalized = TRUE)
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graphxy <- igraph::layout_with_graphopt(graph, charge=0.30, mass=30)
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# Generate color palette:
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colors = heat.colors(
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max(igraph::degree(graph)+1)
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)[igraph::degree(graph)+1]
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plot(
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graph,
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layout=graphxy,
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rescale=TRUE, # Default is true, explicit as reminder.
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vertex.size = (125 * degrees),
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vertex.color = colors,
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vertex.label=NA
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)
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legend(
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"topright",
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legend=c(max(igraph::degree(graph)), 0),
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fill=c(colors[which.max(igraph::degree(graph))], colors[1]),
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title = "Degrees"
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)
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sealKey()
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}
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generate_log_freq_vs_log_rank <- function() {
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sealKey()
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scCCnet <- readRDS("./data/scCCnet.rds") # S. cerevisiae Cell Cycle network
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scCCnet_ns <- scCCnet[-3] # Remove scores
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graph <- igraph::graph_from_edgelist(as.matrix(scCCnet_ns), directed = FALSE)
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degrees <- igraph::degree(graph, normalized = FALSE)
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freqs <- table(degrees)
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scatter.smooth(log10(as.numeric(names(freqs)) + 1),
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log10(as.numeric(freqs)), type = "b",
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bg = "#A5F5CC",
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xlab = "log(Rank)", ylab = "log(frequency)",
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main = "Log Frequency against Log-Rank")
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sealKey()
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}
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get_top_degrees <- function(n = 5) {
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sealKey()
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scCCnet <- readRDS("./data/scCCnet.rds") # S. cerevisiae Cell Cycle network
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scCCnet_ns <- scCCnet[-3] # Remove scores
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graph <- igraph::graph_from_edgelist(as.matrix(scCCnet_ns), directed = FALSE)
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degrees <- igraph::degree(graph, normalized = FALSE)
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sorted_degrees <- degrees[order(degrees)]
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sealKey()
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tail(sorted_degrees, n)
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}
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get_bot_degrees <- function(n = 5) {
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sealKey()
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scCCnet <- readRDS("./data/scCCnet.rds") # S. cerevisiae Cell Cycle network
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scCCnet_ns <- scCCnet[-3] # Remove scores
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graph <- igraph::graph_from_edgelist(as.matrix(scCCnet_ns), directed = FALSE)
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degrees <- igraph::degree(graph, normalized = FALSE)
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sorted_degrees <- degrees[order(degrees)]
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sealKey()
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head(sorted_degrees, n)
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}
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