Plot Correlation Summary from Exposure-Feature Correlations

Generates a bar plot summary of exposure-feature correlations using customizable modes.

Usage

plot_correlation_summary(
  expomicset,
  feature_type = c("degs", "omics", "factors", "factor_features", "exposures", "pcs"),
  mode = c("top_exposures", "top_features", "exposure_category", "assay", "summary"),
  top_n = 15
)

Arguments

expomicset

A MultiAssayExperiment object with correlation results in metadata.

feature_type

One of "degs", "factors", "omics", or "exposures".

mode

One of:

• "top_exposures": Top exposures by assay

• "top_features": Top features by exposure category

• "exposure_category": Total associations by exposure category

• "assay": Total associations by omics assay

• "summary": Patchwork layout combining all

top_n

Number of top exposures or features to display (for top modes). Default is 15.

Value

A ggplot2 object or a patchwork object (if mode = "summary").

Examples

# create example data
mae <- make_example_data(
    n_samples = 10,
    return_mae = TRUE
)
#> Ensuring all omics datasets are matrices with column names.
#> Creating SummarizedExperiment objects.
#> Creating MultiAssayExperiment object.
#> MultiAssayExperiment created successfully.

# correlate with exposures
mae <- mae |>
    run_correlation(
        feature_type = "omics",
        variable_map = mae |>
            pivot_feature() |>
            dplyr::select(
                variable = .feature,
                exp_name = .exp_name
            ),
        exposure_cols = c("exposure_pm25", "exposure_no2", "age", "bmi")
    )
#> Log2-Transforming each assay in MultiAssayExperiment.

# create the correlation summary plot
cor_summary_plot <- mae |>
    plot_correlation_summary(
        feature_type = "omics",
        mode = "summary"
    )