pathway.structure.plot: Extensions to iGraph for Plotting Pathway Structure

In TomKellyGenetics/pathway.structure.permutation: Extensions to iGraph for Testing Pathway Structure

Description

Functions to plot outcomes for testing pathway structure with permutation analysis.

Usage

pathway_perm_plot_density(table_obj, method = "absolute", main = NULL,
  sub = NULL, xlab = "up - down events", ylab = "density", xlim = NULL,
  ylim = NULL, cex.lab = 1, guide = TRUE, legend = TRUE,
  annotate = TRUE, cex.legend = 1, cex.annotation = 1, col = "black")

pathway_perm_lines_density(table_obj, method = "absolute", col = "black")

pathway_perm_plot_raw(table_obj, main = NULL, sub = NULL,
  xlab = "up events", ylab = "down events", cex.lab = 1, col = "black",
  cex = 1, pch = 1)

permutation.structure.proportion(table_obj, method = "absolute")

Arguments

table_obj	List. Output of pathway.structure
method	Specifies metric for comparision of up and down events: "absolute" (1) for difference or "relative" (2) ratio. May be given as a character or numeric input. Defaults to absolute.
main, sub, xlab, ylab, xlim, ylim, cex.lab, col, cex, pch	Arguments to pass on to plot or plot.density
guide, legend, annotate	Logical. Whether guide lines, legend, or p-value annotation is included on the density plot. Default to TRUE.
cex.legend, cex.annotation	numeric. Relative expansion of legend and annotation test in density plot.

Examples

#generate example graphs
library("igraph")
graph <- make_graph(unlist(lapply(letters, function(x) rep(x, 2)))[2:51], directed = TRUE)
plot(graph)

#Example states
test.structure(graph, "a", "c")
source <- sample(letters, 10)
target <- sample(letters, 10)
V(graph)$color <- ifelse(names(V(graph)) %in% source, "lightblue", "grey75")  
V(graph)$color <- ifelse(names(V(graph)) %in% target, "palevioletred", V(graph)$color)  
V(graph)$color <- ifelse(names(V(graph)) %in% intersect(source, target),
                         "mediumpurple2", V(graph)$color)  
plot(graph, layout = layout.fruchterman.reingold, vertex.color= V(graph)$color, 
    vertex.label.family = "mono", vertex.size = 10, vertex.label.color = "black", 
    vertex.frame.color= "grey50", main = graph$name)
matrix.structure(graph, source, target)
table(matrix.structure(graph, source, target))
perm_table <- permutation.structure(graph, source, target, letters)

#Plot Density Output of Permutation Test
pathway_perm_plot_density(perm_table)

#Plot Density Output of Permutation Test
perm_table <- permutation.structure(graph, source, target, letters)
pathway_perm_plot_density(perm_table)
perm_table2 <- permutation.structure(graph, source, target, letters, fixed_intersect = TRUE)
pathway_perm_lines_density(perm_table2, col="lightblue")

#Plot Raw Output of Permutation Test
pathway_perm_plot_raw(perm_table)

permutation.structure.proportion(perm_table) # defaults to absolute
permutation.structure.proportion(perm_table, method = "relative")

TomKellyGenetics/pathway.structure.permutation documentation built on May 9, 2019, 4:53 p.m.