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Plot an ORA term-feature community network

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

Builds a deterministic community layout from explicitly selected ORA terms and their enriched-feature membership. Term-to-term edges represent the Jaccard coefficient of the complete enriched-feature sets, not ontology or full-pathway similarity. A shared feature is drawn once inside every selected term community that contains it, matching the reference community grammar. Optional feature values control every corresponding visual node's size and alpha by absolute magnitude. Values do not affect term selection.

Usage

plot_ora_network(
  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_radial(), plot_qc_correlation(), plot_qc_library(), plot_qc_outliers(), plot_save(), theme_bulkmae()