Construct an interactive pathway network visualization

Builds a self-contained data payload and an interactive D3 visualization for selected pathways across spatial clusters. Topology lookup, edge preparation, differential-expression matching, and matrix extraction are indexed so they are not repeated for every cluster-pathway pair.

Usage

PathwayNetworkPlots(
  SpaMTP,
  ident,
  regpathway,
  DE.list,
  selected_pathways = NULL,
  path = getwd(),
  SM_slot = "counts",
  ST_slot = "counts",
  colour_palette = NULL,
  SM_assay = "SPM",
  ST_assay = "SPT",
  analyte_types = c("genes", "metabolites"),
  annotation_source = c("current", "auto", "legacy"),
  annotation_score_threshold = NULL,
  annotation_score_floor = 0.01,
  metabolite_detection = c("leading_edge", "annotated"),
  image = "slice1",
  verbose = TRUE,
  top_n_pathways = 10L,
  max_nodes = 500L,
  label_mode = c("detected", "all", "none"),
  max_spatial_points = 50000L,
  layout_mode = c("repulsion", "force", "radial", "bipartite")
)

Arguments

SpaMTP

A SpaMTP Seurat object containing spatial metabolomics and/or spatial transcriptomics data. Metabolomics data must first be annotated by AnnotateSM().

ident

Metadata column used to identify spatial clusters or regions.

regpathway

Data frame returned by FindRegionalPathways().

DE.list

One differential-expression data frame per requested analyte type. Data frames must contain cluster, gene, avg_log2FC (or logFC), and p_val_adj (or FDR). A named list is recommended.

selected_pathways

Optional pathway names or source IDs. Matching is case-insensitive. When NULL, the most important pathways are selected by summed absolute NES.

path

Output directory for the generated HTML file.

SM_slot

Layer containing spatial-metabolomics values.

ST_slot

Layer containing spatial-transcriptomics values.

colour_palette

Colours used for the spatial abundance raster.

SM_assay

Spatial-metabolomics assay name.

ST_assay

Spatial-transcriptomics assay name.

analyte_types

One or both of "genes" and "metabolites".

annotation_source

Metabolite annotation provenance. The default, "current", requires the indexed, scored RaMP annotation output. "auto" permits a warned legacy fallback and "legacy" requests it explicitly.

annotation_score_threshold

Minimum indexed annotation score used for metabolite matching. When NULL, the threshold recorded by FindRegionalPathways() is reused (default = NULL).

annotation_score_floor

Lowest annotation score embedded in the HTML for interactive filtering. It is automatically lowered when the initial annotation_score_threshold is smaller (default = 0.01).

metabolite_detection

Which metabolite nodes receive detected styling. "leading_edge" uses only GSEA leading-edge metabolites; "annotated" also includes every score-filtered annotation belonging to the selected pathway, regardless of DE significance.

image

Spatial image/FOV passed to Seurat::GetTissueCoordinates().

verbose

Display progress messages.

top_n_pathways

Number of pathways selected when selected_pathways is NULL.

max_nodes

Maximum number of nodes per cluster-pathway view. Detected leading-edge analytes are always retained, followed by their neighbours and high-degree nodes. Use Inf to disable pruning.

label_mode

Initial node-label mode: detected nodes only, all nodes, or no labels. It can also be changed interactively.

max_spatial_points

Maximum number of spatial points embedded in the HTML. Larger datasets are deterministically downsampled for responsive browser rendering. Use Inf to retain all points.

layout_mode

Initial network layout. "repulsion" maximises spacing, "force" uses a balanced force-directed layout, "radial" separates analyte classes into rings, and "bipartite" separates genes and metabolites vertically. It can also be changed interactively.

Value

Invisibly returns the generated HTML file path.

Examples

# PathwayNetworkPlots(
#   SpaMTP, ident = "Custom_ident", regpathway = regpathway,
#   DE.list = DE.list, selected_pathways = "WP1902"
# )