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Plot an ORA radial term-feature network

Source: R/plotting-ora.R
plot_ora_radial.Rd

Places terms on an inner ring and unique enriched features on an outer ring. Membership curves retain every selected term-feature relation and inner term-edge width and alpha show the number of shared enriched features. For layout only, each outer feature is assigned to the most significant adjacent term, with selected-term order breaking ties; shared features remain connected to every adjacent term.

Usage

plot_ora_radial(
  result,
  terms,
  membership = NULL,
  feature_values = NULL,
  features = NULL,
  term_labels = NULL,
  feature_labels = NULL,
  label_features = NULL,
  p_value = c("auto", "adjusted", "raw")
)

Arguments

result

A clusterProfiler enrichResult or compatible ORA result data frame. See plot_ora_bubble().

terms

Unique term identifiers to display, in the desired order.

membership

Optional term-named list of enriched feature identifiers. When omitted, membership is read from the result's geneID column. An explicit list must describe the selected terms exactly.

feature_values

Optional feature-named finite numeric vector. It must cover every displayed feature; additional values are ignored.

features

Optional explicit feature identifiers to display. Supply a character vector for one global feature set, or a term-named list to select displayed membership independently within each selected term. NULL displays all enriched features. Selection never changes overlap statistics computed from the complete membership.

term_labels

Optional complete term-named labels.

feature_labels

Optional feature-named labels covering every displayed feature. Additional labels are ignored.

label_features

Explicit displayed feature identifiers to label. NULL labels no feature nodes.

p_value

Evidence column used for term-node size.

Value

An unprinted standard ggplot object carrying recommended physical dimensions for plot_save().

See also

Other plotting: plot_assay_heatmap(), plot_de_ma(), plot_de_volcano(), plot_embedding(), plot_gsea_classic(), plot_gsea_ridge(), plot_ora_bubble(), plot_ora_network(), plot_qc_correlation(), plot_qc_library(), plot_qc_outliers(), plot_save(), theme_bulkmae()