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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).

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.

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; if NULL, uses ggsci::pal_npg().

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.

Examples

# Plot a Manhattan summary from ExWAS results
# plot_manhattan(mae, pval_thresh = 0.01)