go_plot: Visualise reduced pathway enrichments
In RHReynolds/rutils: Common utility functions

View source: R/go_plot.R

go_plot

R Documentation

Visualise reduced pathway enrichments

Description

go_plot plots GO terms that have been reduced using go_reduce.

Usage

go_plot(
  reduced_pathway_df,
  col_gene_list = "gene_list",
  col_fdr = "fdr",
  fct_gene_list = NULL
)

Arguments

`reduced_pathway_df`	the tibble derived from `go_reduce`.
`col_gene_list`	a `character()` vector, with the name of column containing the name(s) of the inputted gene list(s). Defaults to `"gene_list"`.
`col_fdr`	a `character()` vector, with the name of column containing enrichment p-values/fdr-values. Defaults to `"fdr"`.
`fct_gene_list`	a `character()` vector, with the order in which input gene lists should be factored. Defaults to NULL.

Value

ggplot displaying the pathway enrichments using reduced perent terms.

x-axis displays the inputted gene list(s).
y-axis displays the reduced parent term, with the number of associated child GO terms in brackets. Parent terms are ordered first by the factoring of the input gene list (as provided in the argument, fct_gene_list) and then by the number of associated child terms.
size of the dot indicates the proportion of child terms associated with an inpute gene list that are annotated to the parent term.
fill of dot indicates the minimum FDR assigned to a child term that is associated with the parent term (within an input gene list).

Examples

file_path <-
    system.file(
        "testdata",
        "go_test_data.txt",
        package = "rutils",
        mustWork = TRUE
    )

pathway_df <-
    readr::read_delim(file_path,
        delim = "\t"
    ) %>%
    dplyr::mutate(
        gene_list = c(rep("a", 5), rep("b", 5)),
        fdr = runif(10, min = 0, max = 0.05)
    )

reduced_pathway_df <-
    go_reduce(
        pathway_df = pathway_df,
        threshold = 0.9,
        scores = NULL,
        measure = "Wang"
    )

go_plot(
    reduced_pathway_df,
    col_gene_list = "gene_list",
    col_fdr = "fdr",
    fct_gene_list = c("b", "a")
)

RHReynolds/rutils documentation built on March 26, 2022, 8:17 a.m.