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Plot a Manhattan-style ExWAS summary across omics categories

Source: R/plot_manhattan.R
plot_manhattan.Rd

This function generates a multi-faceted Manhattan plot from the results of associate_all_outcome(), visualizing the significance of associations across omics features, grouped by category. Significant features can be highlighted and labeled, and strip backgrounds can be colored per facet.

Usage

plot_manhattan(
  expomicset,
  pval_thresh = 0.05,
  feature_col = "term",
  alpha = 0.5,
  min_per_cat = 1,
  vars_to_label = NULL,
  sig_color = "magenta2",
  non_sig_cols = c("grey25", "grey75"),
  pval_thresh_line_col = "grey25",
  panel_sizes = c(1, 1, 1, 1, 1),
  linetype = "dashed",
  facet_cols = NULL,
  label_size = 3.5,
  facet_angle = 90,
  facet_text_face = "bold.italic"
)

Arguments

expomicset

A MultiAssayExperiment object that has already been processed by associate_all_outcome().

pval_thresh

Numeric threshold for significance (default = 0.05).

feature_col

A character string indicating the column name to use for feature labeling and highlighting (e.g., "term" or "feature"). Default is "term".

alpha

Transparency applied to facet strip colors (default = 0.5).

min_per_cat

Minimum number of features per category to be shown (default = 1).

vars_to_label

Optional character vector of variable names to label explicitly, matched against the feature_col column.

sig_color

Color used for significant points (default = "magenta2").

non_sig_cols

Character vector of alternating colors for non-significant points (default = c("grey25", "grey75")).

pval_thresh_line_col

Color of the horizontal significance threshold line (default = "grey25").

panel_sizes

Numeric vector passed to ggh4x::force_panelsizes() to control panel widths (default = c(1,1,1,1,1)).

linetype

Line type for the horizontal threshold (default = "dashed").

facet_cols

Optional vector of colors to use for facet strip backgrounds.

label_size

Numeric size of the feature label text (default = 3.5).

facet_angle

Angle (in degrees) for strip text rotation (default = 90).

facet_text_face

Font face for facet strip labels (default = "bold.italic").

Value

A ggplot object showing the Manhattan-style faceted plot.

Details

  • This function expects associate_all_outcome() to have been run first.

  • Facets represent omics categories, and points represent features.

  • Points below the significance threshold are colored using non_sig_cols, while significant ones are colored with sig_color and optionally labeled.

  • Uses ggrepel to avoid overlapping labels and ggh4x for enhanced faceting.

  • The feature_col argument allows customization of which column is used to label or identify features, enabling compatibility with different result formats.

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.

# run association tests
mae <- mae |>
    run_association(
        source = "omics",
        top_n = 20,
        feature_set = c("exposure_pm25", "exposure_no2"),
        outcome = "smoker",
        covariates = c("age"),
        family = "binomial"
    )
#> Log2-Transforming each assay in MultiAssayExperiment.
#> Scaling each assay in MultiAssayExperiment.
#> Running GLMs.
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred

# create the manhattan plot
manhattan_p <- mae |>
    plot_manhattan(feature_col = "term")