Visualize network with custom layouts in different samples

Usage

ggNetView_multi(
  mat,
  group_info,
  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"),
  shape = 21,
  pointalpha = 1,
  pointsize = c(1, 10),
  pointstroke = 0.3,
  pointlabel = NULL,
  pointlabelsize = 5,
  group.by = "Modularity",
  fill.by = "Modularity",
  color.by = NULL,
  fill = NULL,
  color = NULL,
  jitter = FALSE,
  jitter_sd = 0.1,
  plot_line = TRUE,
  mapping_line = FALSE,
  curve = F,
  curvature = 0.25,
  linealpha = 0.25,
  linecolor = "grey70",
  label = FALSE,
  labelsize = 10,
  labelsegmentsize = 1,
  labelsegmentalpha = 1,
  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,
  add_outer = FALSE,
  q_outer = 0.88,
  expand_outer = 1.02,
  outerwidth = 1.25,
  outerlinetype = 2,
  outeralpha = 0.5,
  nodelabsize = 5,
  remove = FALSE,
  dropOthers = FALSE,
  orientation = "up",
  angle = 0,
  scale = T,
  anchor_dist = 6,
  layout_nrow = NULL,
  layout_ncol = NULL,
  seed = 1115,
  nrow = NULL,
  ncol = NULL
)

Arguments

mat: Numeric matrix. A numeric matrix with samples in rows and variables in columns.
group_info: DataFrame The group information contains: Sample and Group
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: p.threshold 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`
shape: Integer (default = 21). The point shape likely in ggplot2.
pointalpha: Integer (default = 1). The point alpha
pointsize: Vector (default = c(1,10)) The point size rang.
pointstroke: Integer (default = 0.3).
pointlabel: Character (default = NULL). Optional node label mode for top Degree nodes within each module. Supported values: "topN" (e.g. "top1", "top7", "top20") and "ALL".
pointlabelsize: Integer (default = 5). Change point label size.
group.by: Character (default = "Modularity"). Change group for nodes
fill.by: Character (default = "Modularity"). Change fill for nodes
color.by: Character (default = NULL). Change color for nodes
fill: Named vector of colors for node fill. If NULL (default), uses scale_fill_ggnetview; if provided, uses scale_fill_manual(values = fill).
color: Named vector of colors for node/edge/label color. If NULL (default), uses scale_color_ggnetview; if provided, uses scale_color_manual(values = color).
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`.
plot_line: Logical (default = TRUE). Whether to plot line in net plot.
mapping_line: Logical (default = FALSE). Whether to mapping line in ggNetView.
curve: Logical (default = FALSE). Whether to plot curve line in net plot.
curvature: Integer (default = 0.25) The curve level of curve line when curve is TRUE
linealpha: Integer (default = 0.25). Change line alpha.
linecolor: Character (default = "grey70"). Change line color.
label: Logical or Character (default = FALSE). Whether to display module labels. If a character string, used as legend prefix.
labelsize: Integer (default = 10). Change Module label size.
labelsegmentsize: Integer (default = 1). Change label segment size.
labelsegmentalpha: Integer (default = 1). Change label segment alpha.
add_group_outer: Logical (default = FALSE). Whether to add a circle boundary around the entire network (mimics ggforce::geom_mark_circle).
add_group_outer_expand: Numeric (default = 2). Expansion in mm for the group circle; passed to geom_mark_circle(expand = ...).
add_group_outer_color: Character (default = "grey50"). Color of the group outer circle border.
add_group_outer_fill: Character or NULL (default = NULL). Fill color of the group outer circle. NULL = no fill (transparent).
add_group_outer_fill_alpha: Numeric (default = 0.2). Alpha (transparency) of the group outer circle fill.
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.
add_outer: Logical (default = FALSE). Whether to add an outer circle/border around each module.
q_outer: Numeric (default = 0.88). Quantile of radial distance used to construct the smooth outer boundary for each module.
expand_outer: Numeric (default = 1.02). Global scaling factor applied to the smoothed radial distances when drawing the outer boundary.
outerwidth: Integer (default = 1.25). Change outer linewidth.
outerlinetype: Integer (default = 2). Change outer linetype.
outeralpha: Integer (default = 0.5). Change outer alpha.
nodelabsize: Integer (default = 5). Change node label size.
remove: Logical (default = FALSE). Remove nodes that are not modules.
dropOthers: Logical (default = FALSE). If TRUE, remove nodes in the "Others" module before layout and visualization.
orientation: Character string. Custom orientation; one of "up","down","left","right".
angle: Integer (default = 0). Change orientation angle.
scale: Logical (default = T). modules applicable to `Bipartite, Tripartite, Quadripartite, Multipartite, Pentapartite Layout` to scale the radius
anchor_dist: Integer (default = 6) the distance of each modules, applicable to `Bipartite, Tripartite, Quadripartite, Multipartite, Pentapartite Layout`
layout_nrow: Integer (default = NULL). Number of layout rows passed to ggNetView when using consensus-module grid layouts.
layout_ncol: Integer (default = NULL). Number of layout columns passed to ggNetView when using consensus-module grid layouts.
seed: Integer (default = 1115). Random seed for reproducibility.
nrow: Integer (default = NULL). Number of rows in the combined patchwork plot.
ncol: Integer (default = NULL). Number of columns in the combined patchwork plot.

Value

A ggplot object representing the network visualization.

Examples

NULL
#> NULL