Visualize pathway enrichments as network.

plot_pareg_with_args(
  x,
  show_term_names = TRUE,
  min_similarity = 0,
  term_subset = NULL
)

Arguments

x

An object of class pareg.

show_term_names

Whether to plot node labels.

min_similarity

Don't plot edges for similarities below this value.

term_subset

Subset of terms to show.

Value

ggplot object.

Examples

df_genes <- data.frame(
  gene = paste("g", 1:20, sep = ""),
  pvalue = c(
    rbeta(10, .1, 1),
    rbeta(10, 1, 1)
  )
)
df_terms <- rbind(
  data.frame(
    term = "foo",
    gene = paste("g", 1:10, sep = "")
  ),
  data.frame(
    term = "bar",
    gene = paste("g", 11:20, sep = "")
  )
)
fit <- pareg(df_genes, df_terms, max_iterations = 10)
plot(fit)