Plot Exposure-Omics Associations — plot_exposure_omics

Plots the number of significant exposure-omics associations, grouped either by exposure or the exposure category.

Usage

plot_exposure_omics_association(
  exposomicset,
  plot_type = c("exposures", "category"),
  pval_col = "p_adjust",
  pval_thresh = 0.05
)

Arguments

exposomicset: A MultiAssayExperiment object containing association results.
plot_type: Character. One of "exposures" or "category". Controls whether associations are summarized per exposure or per exposure category. Defaults to "exposures".
pval_col: Character. Name of the column used for p-value filtering. Defaults to "p_adjust".
pval_thresh: Numeric. Significance threshold applied to pval_col. Rows with values below this threshold are retained. Defaults to 0.05.

Value

A ggplot object.

Examples

# create example data
mae <- make_example_data(
    n_samples = 20,
    return_mae = TRUE
)
#> Ensuring all omics datasets are matrices with column names.
#> Creating SummarizedExperiment objects.
#> Creating MultiAssayExperiment object.
#> MultiAssayExperiment created successfully.

# run exposure-omics association
mae <- mae |>
    run_exposure_omics_association(
        exposures = c("exposure_pm25", "exposure_no2"),
        covariates = c("age", "sex")
    )
#> Testing 2 exposures across 2 assays
#> Processing assay: mRNA
#> Processing assay: proteomics

plot_exposure_omics_association(
    exposomicset = mae,
    plot_type = "exposures"
)