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Visualize multiple networks and show the connections between them to highlight key members within the networks

Source: R/ggNetView_multi_link.R
ggNetView_multi_link.Rd

Provide either (mat, group_info) or graph_obj_list as input. When graph_obj_list is provided, mat and group_info are ignored.

Usage

ggNetView_multi_link(
  mat = NULL,
  group_info = NULL,
  graph_obj_list = NULL,
  transfrom.method = c("none", "scale", "center", "log2", "log10", "ln", "rrarefy",
    "rrarefy_relative"),
  r.threshold = 0.7,
  p.threshold = 0.05,
  method = c("WGCNA", "SpiecEasi", "SPARCC", "cor"),
  cor.method = c("pearson", "kendall", "spearman"),
  proc = c("holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none"),
  module.method = c("Fast_greedy", "Walktrap", "Edge_betweenness", "Spinglass"),
  SpiecEasi.method = c("mb", "glasso"),
  sparcc_R = 20,
  node_annotation = NULL,
  top_modules = 15,
  layout = NULL,
  node_add = 7,
  ring_n = NULL,
  r = 1,
  center = TRUE,
  idx = NULL,
  shrink = 1,
  k_nn = 12,
  push_others_delta = 0,
  layout.module = c("random", "adjacent", "order"),
  group.by = "Modularity",
  fill.by = "Modularity",
  fill = NULL,
  color = NULL,
  pointsize = c(1, 5),
  jitter = FALSE,
  jitter_sd = 0.01,
  mapping_line = FALSE,
  linealpha = 0.25,
  linecolor = "grey70",
  inner_curve = FALSE,
  inner_curvature = 0.12,
  inner_curve_adaptive = TRUE,
  inner_curve_adaptive_range = c(0.7, 1.3),
  inner_curve_adaptive_bins = 7,
  add_outer = "circle",
  q_outer = 0.88,
  expand_outer = 1.02,
  outerwidth = 1.25,
  outerlinetype = 2,
  outeralpha = 0.5,
  link_level = "Module",
  link_curve = FALSE,
  link_curvature = 0.2,
  link_curve_mode = "outward",
  link_curve_adaptive = TRUE,
  link_curve_adaptive_range = c(0.7, 1.3),
  link_curve_adaptive_bins = 7,
  link_color_node = NULL,
  link_color_module = NULL,
  link_linewidth_node = 1,
  link_linewidth_module = 1,
  link_linetype_node = 2,
  link_linetype_module = 1,
  link_linealpha_node = 0.25,
  link_linealpha_module = 0.5,
  dropOthers = FALSE,
  calculate_topology = FALSE,
  comparisons = TRUE,
  comparisons_groups = NULL,
  order = NULL,
  group_layout = "circle",
  scale_groups = TRUE,
  orientation = "up",
  angle = 0,
  anchor_dist = 6,
  layout_anchor_dist = NULL,
  nrow = NULL,
  ncol = NULL,
  sine_period = 4,
  label_offset = 0.2,
  label_size = 4,
  add_group_outer = FALSE,
  add_group_outer_expand = 2,
  add_group_outer_color = "grey50",
  add_group_outer_fill = NULL,
  add_group_outer_fill_alpha = 0.2,
  add_group_outer_linetype = 1,
  add_group_outer_linewidth = 0.5,
  seed = 1115
)

Arguments

mat

Numeric matrix. Required when graph_obj_list is NULL. A numeric matrix with variables (e.g. genes, taxa) in rows and samples in columns.

group_info

DataFrame. Required when graph_obj_list is NULL. The group information contains: Sample and Group. If Sample or Group contain underscores (_), they are automatically replaced with hyphens (-) to avoid parsing issues; mat column names, order, and comparisons_groups are updated accordingly.

graph_obj_list

Named list of tbl_graph objects. Alternative to mat and group_info. Each element is a graph object (e.g. from build_graph_from_mat or build_graph_from_df). List names define group names (e.g. list(WT = g1, KO = g2)). When provided, mat and group_info are ignored. Enables custom pre-built networks.

transfrom.method

Character. Data transformation methods applied before correlation analysis. Options include: "none" (raw data), "scale" (z-score standardization), "center" (mean centering only), "log2" (log2 transfrom), "log10" (log10 transfrom), "ln" (natural transfrom ), "rrarefy" (random rarefaction using vegan::rrarefy), "rrarefy_relative" (rarefy then convert to relative abundance).

r.threshold

Numeric. Correlation coefficient threshold; edges are kept only if |r| >= r.threshold.

p.threshold

Numeric. #' Significance threshold for correlations; edges are kept only if p < p.threshold.

method

Character. Relationship analysis methods. Options include: "WGCNA", "SpiecEasi", "SPARCC" and "cor".

cor.method

Character. Correlation analysis method. Options include "pearson", "kendall", and "spearman".

proc

Character. Correlation p-value adjustment methods. Options include: "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", and "none".

module.method

Character. Network community detection (module identification) method. Options include "Fast_greedy", "Walktrap", "Edge_betweenness", and "Spinglass".

SpiecEasi.method

Character. Method used in SpiecEasi network inference; options include "mb" and "glasso".

sparcc_R

Integer. Number of bootstrap/permutation replicates for SparCC p-values (when method = "SPARCC"). Default 20.

node_annotation

Data frame. Optional node annotation table, containing metadata such as taxonomy or functional categories.

top_modules

Integer. Number of top-ranked modules to retain for downstream visualization or analysis.

layout

Character string. Custom layouts; one of "gephi", "square", "square2", "petal", "petal2", "heart_centered","diamond", "star", "star_concentric","rectangle, "rightiso_layers" etc.

node_add

Integer (default = 7). Number of nodes to add in each layer of the layout.

ring_n

Numeric (default = 7) Numbers of ring in rings layout.

r

Numeric (default = 1). Radius increment for concentric or layered layouts.

center

Logical (default = TRUE). Whether to place a node at the center of the layout.

idx

Optional. Index of nodes to be emphasized or centered in the layout

shrink

Numeric (default = 1). Shrinkage factor applied to the center points.

k_nn

Numeric (default = 8). Number of nearest neighbors used to build the local adjacency graph.

push_others_delta

Numeric (default = 0). Radial offset applied to the "Others" module to slightly

layout.module

Character (default = "random") - random : modules are distributed more randomly and independently. - adjacent : modules are positioned close to each other, minimizing inter-module gaps. - order : modules are distributed by order, applicable to `Bipartite, Tripartite, Quadripartite, Multipartite, Pentapartite Layout`

group.by

Character (default = "Modularity"). Change group for nodes

fill.by

Character (default = "Modularity"). Change fill for nodes

fill

Named vector of colors for node/module fill (e.g. c("M1" = "red", "M2" = "blue")). If NULL (default), uses viridis discrete fill scale (scale_fill_viridis_d); if provided, uses scale_fill_manual(values = fill).

color

Color setting for node/module border. Supports either a single color string (fixed border color) or a named vector (module-to-color mapping, similar to fill). If NULL, mapped borders use viridis discrete color scale (scale_color_viridis_d).

pointsize

Numeric vector of length 2 (default = c(1, 5)). The range of point size when mapping Degree to size. First value is minimum size, second is maximum size.

jitter

Logical (default = FALSE). Whether to apply jitter to points.

jitter_sd

Integer (default = 0.1). The standard deviation of the jitter applied when `jitter = TRUE`.

mapping_line

Logical or Character (default = FALSE). Whether to map line color in ggNetView. If a character string is provided, it must be a variable name in edge data.

linealpha

Integer (default = 0.25). Change line alpha.

linecolor

Character (default = "grey70"). Change line color.

inner_curve

Logical (default = FALSE). Whether to draw within-group edges as curves.

inner_curvature

Numeric (default = 0.12). Curvature for within-group edges when inner_curve = TRUE.

inner_curve_adaptive

Logical (default = TRUE). Whether to adapt within-group edge curvature by edge length when inner_curve = TRUE.

inner_curve_adaptive_range

Numeric vector of length 2 (default = c(0.7, 1.3)). Multipliers applied to inner_curvature for shortest and longest within-group edges.

inner_curve_adaptive_bins

Integer (default = 7). Number of bins used to approximate per-edge adaptive curvature for within-group edges.

add_outer

Logical or Character (default = "circle"). Add outer boundaries for matched modules. Supported values: "circle" (use ggforce::geom_mark_circle), "manual" (use smoothed polygon boundary like ggNetView), and "none" (disable). Logical TRUE/FALSE are accepted and mapped to "circle"/"none".

q_outer

Numeric (default = 0.88). Quantile of radial distance used to construct the smooth outer boundary when add_outer = "manual".

expand_outer

Numeric (default = 1.02). Global scaling factor applied to the smooth outer boundary when add_outer = "manual".

outerwidth

Numeric (default = 1.25). Line width for module outer boundaries.

outerlinetype

Integer or character (default = 2). Linetype for module outer boundaries (e.g. 1 = solid, 2 = dashed).

outeralpha

Numeric (default = 0.5). Alpha for module outer boundaries.

Character (default = "Module"). Cross-group link granularity. One of "None", "Module", "Node", "NodeinModule", "Module&Node", or "Module&Node2". "None" draws no cross-group links. "Module" links significant module matches (module centroids). "Node" links shared node names across groups. "NodeinModule" links both module centroids and nodes within significantly overlapping modules (module links show which modules overlap; node links show shared nodes). "Module&Node" draws both module-level links and node-level links. "Module&Node2" same as "Module&Node" but adds outer boundaries for all modules (not only matched ones).

Logical (default = FALSE). Whether to draw cross-group links as curves (geom_curve) instead of straight segments.

Numeric (default = 0.2). Curvature used when link_curve = TRUE.

Character (default = "outward"). Curve direction strategy used when link_curve = TRUE. "outward" bends links away from the global center. "inward" bends links toward the global center. "cross" follows a cross-axis rule: left links bend left, right links bend right, upper links bend up, and lower links bend down.

Logical (default = TRUE). Whether to adapt link curvature by link length when link_curve = TRUE. Longer links get larger curvature and shorter links get smaller curvature.

Numeric vector of length 2 (default = c(0.7, 1.3)). Multipliers applied to link_curvature for shortest and longest links. The first value is the minimum multiplier; the second is the maximum multiplier.

Integer (default = 7). Number of bins used to approximate per-link adaptive curvature.

Character or NULL (default = NULL). Colors for node-to-node cross-group links. NULL = use default palette. A single value, named vector (e.g. c("WT|KO" = "red")), or unnamed vector (by pair index).

Character or NULL (default = NULL). Colors for module-to-module cross-group links. Same rules as link_color_node.

Numeric (default = 1). Line width for node-to-node cross-group links. Single value or vector (by pair index/named).

Numeric (default = 1). Line width for module-to-module cross-group links. Single value or vector.

Integer or character (default = 2). Linetype for node-to-node cross-group links (e.g. 2 = dashed, 1 = solid). Single value or vector.

Integer or character (default = 1). Linetype for module-to-module cross-group links. Single value or vector.

Numeric (default = 0.25). Alpha (transparency) for node-to-node cross-group links. Single value or vector.

Numeric (default = 0.5). Alpha (transparency) for module-to-module cross-group links. Single value or vector.

dropOthers

Logical (default = FALSE). If TRUE, remove nodes in the "Others" module from each group's graph_obj before layout, plotting, and module-overlap comparison.

calculate_topology

Logical (default = FALSE). Whether to compute topology for each group using get_network_topology_parallel() and get_sample_subgraph_topology_parallel().

comparisons

Logical (default = TRUE). Whether to perform cross-group comparisons and draw links. If FALSE, no module overlap or node comparison is done, and no cross-group links are drawn.

comparisons_groups

List or NULL (default = NULL). When comparisons = TRUE, constrains which group pairs are compared. Each element must be a length-2 character vector, e.g. list(c("WT", "OE"), c("WT", "KO")). Group names must exist in group_info$Group or names(graph_obj_list). If NULL, all pairwise group comparisons are performed.

order

Character vector or NULL (default = NULL). Order of groups for layout positions. Groups are placed evenly on a circle: 1st = top, 2nd = next clockwise, etc. (e.g. 3 groups = triangle, 4 = square). Must contain all unique groups from group_info$Group or names(graph_obj_list) exactly once. If NULL, uses unique(group_info$Group) or names(graph_obj_list) order (first occurrence).

group_layout

Character (default = "circle"). Arrangement of groups in the multi-group plot. "circle": groups placed evenly on a circle (default). "row": groups in a grid, filled row-by-row; uses nrow and ncol. "column": groups in a grid, filled column-by-column; uses nrow and ncol. "square": 4 groups at corners of a square (top-left, top-right, bottom-right, bottom-left). "diamond": 4 groups at top, right, bottom, left (like a rotated square). "triangle": 3 groups at vertices of an upright triangle (point up). "triangle_down": 3 groups at vertices of an inverted triangle (point down). "snake": groups in a grid with snake-like ordering; first row left-to-right, second row right-to-left, third row left-to-right, etc. Uses nrow and ncol. "snake_vertical": groups along a smooth sine curve; uses sine_period. "snake_vertical_sin": same as "snake_vertical". "snake_vertical_cos": groups along a smooth cosine curve; uses sine_period. "snake_vertical_neg_sin": smooth -sin curve. "snake_vertical_neg_cos": smooth -cos curve. "sin": vertex-only; group 1 at center; groups 2+ alternate peaks and troughs. "cos": vertex-only; group 1 at peak; groups 2+ alternate peak and trough. "-sin": vertex-only; group 1 at center; groups 2+ alternate down, up. "-cos": vertex-only; group 1 at trough; groups 2+ alternate trough and peak. "center_pairs": group 1 at center (y=0); remaining groups form pairs on peak (y=1) and trough (y=-1), with one anchor_dist gap between center and first pair. Pairs alternate right/left of center. If a pair has only one group, it goes on top (peak). Empty pair slots keep their positions.

scale_groups

Logical (default = TRUE). Whether to normalize each group to a comparable coordinate scale before placing groups on anchors for cross-group visual comparison.

orientation

Character string. Custom orientation; one of "up","down","left","right".

angle

Integer (default = 0). Change orientation angle.

anchor_dist

Numeric (default = 6). Distance between groups when placing each group network on the outer circle in ggNetView_multi_link.

layout_anchor_dist

Numeric (default = NULL). Anchor distance passed to the single-group layout function (module spacing within each group). If NULL, it falls back to anchor_dist for backward compatibility.

nrow

Integer (default = NULL). Number of rows. Used by: (1) group_layout = "row", "column", or "snake" for group grid; (2) layout functions like "consensus_module_equal_gephi" for module grid.

ncol

Integer (default = NULL). Number of columns. Used by: (1) group_layout = "row", "column", or "snake" for group grid; (2) layout functions like "consensus_module_equal_gephi" for module grid.

sine_period

Numeric (default = 4). Groups per wavelength for snake_vertical*; ignored for sin, cos, -sin, -cos.

label_offset

Numeric (default = 0.2). Vertical offset of group labels above each group's layout (added to max y).

label_size

Numeric (default = 4). Font size for group labels (Group, Node, Edge, etc.).

add_group_outer

Logical (default = FALSE). Whether to add a circle boundary around each group (mimics ggforce::geom_mark_circle).

add_group_outer_expand

Numeric (default = 2). Expansion in mm for the group circle to account for point size; passed to geom_mark_circle(expand = ...).

add_group_outer_color

Character (default = "grey50"). Color of the group outer circle border. A single value applies to all groups; a named vector maps group names to colors (e.g. c("WT" = "blue", "KO" = "red")); an unnamed vector is used by index (recycled if needed).

add_group_outer_fill

Character or NULL (default = NULL). Fill color of the group outer circle. NULL = no fill (transparent). A single value, named vector, or unnamed vector works like add_group_outer_color.

add_group_outer_fill_alpha

Numeric (default = 0.2). Alpha (transparency) of the group outer circle fill; 0 = fully transparent, 1 = opaque.

add_group_outer_linetype

Integer or character (default = 1). Linetype of the group outer circle (e.g. 1 = solid, 2 = dashed).

add_group_outer_linewidth

Numeric (default = 0.5). Line width of the group outer circle.

seed

Integer (default = 1115). Random seed for reproducibility.

pointstroke

Integer (default = 0.3).

Value

A list containing plot, module-overlap info, link info, group graphs, and optional topology results.

Examples

NULL
#> NULL