plot_pareg_with_args: Plot result of enrichment computation.

In cbg-ethz/pareg: Pathway enrichment using a regularized regression approach

Plot result of enrichment computation.

Description

Visualize pathway enrichments as network.

Usage

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)

cbg-ethz/pareg documentation built on July 20, 2023, 7:30 p.m.