Graphs and networks largely finished.

ABC-units.Rproj

@@ -1,16 +1,16 @@
-Version: 1.0
+Version: 1.0
-
+
-RestoreWorkspace: No
+RestoreWorkspace: No
-SaveWorkspace: No
+SaveWorkspace: No
-AlwaysSaveHistory: No
+AlwaysSaveHistory: No
-
+
-EnableCodeIndexing: Yes
+EnableCodeIndexing: Yes
-UseSpacesForTab: Yes
+UseSpacesForTab: Yes
-NumSpacesForTab: 2
+NumSpacesForTab: 2
-Encoding: UTF-8
+Encoding: UTF-8
-
+
-RnwWeave: knitr
+RnwWeave: knitr
-LaTeX: XeLaTeX
+LaTeX: XeLaTeX
-
+
-AutoAppendNewline: Yes
+AutoAppendNewline: Yes
-StripTrailingWhitespace: Yes
+StripTrailingWhitespace: Yes

myScripts/Graphs_and_networks.R

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

myScripts/genome_annotation.R

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+# Integrator Unit: Genome Annotation
+bio3d::get.seq()