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Visualize network with module-environment heatmaps

Source: R/ggnetview_modularity_heatmaps.R
ggnetview_modularity_heatmaps.Rd

Combines ggNetView network visualization with four environmental correlation heatmaps. Module-environment relationships are computed using module eigengenes (recommended) or module relative abundance, then correlated with environmental factors. Links connect module centroids to heatmap diagonals.

Usage

ggnetview_modularity_heatmaps(
  graph_obj,
  env,
  otu_mat,
  env_select = NULL,
  module_index = c("eigengene", "abundance"),
  abundance_type = c("sum", "mean"),
  relation_method = c("correlation", "mantel"),
  cor.method = c("pearson", "kendall", "spearman"),
  cor.use = c("everything", "all", "complete", "pairwise", "na"),
  mantel.method2 = c("pearson", "kendall", "spearman"),
  drop_nonsig = FALSE,
  layout = "gephi",
  layout.module = c("random", "adjacent", "order"),
  orientation = c("top_right", "bottom_right", "top_left", "bottom_left"),
  distance = 3,
  r = 6,
  HeatmapScale = 1,
  SigLineAlpha = 0.5,
  HeatmapLabelSize = 5,
  HeatmapSigSize = 5,
  HeatmapColorBar = NULL,
  HeatmapLabelOrient = 0,
  SigLineWidth = c(0.5, 2),
  SigLineColor = c("#fdbb84", "#d7301f"),
  HeatmapPointSize = 5,
  HeatmapPointFill = "#de77ae",
  HeatmapTileColor = NA,
  HeatmapTileSize = 0,
  ...
)

Arguments

graph_obj

A graph object from build_graph_from_mat or build_graph_from_df.

env

Data frame or matrix of environmental variables (samples as rows).

otu_mat

Numeric matrix. Rows = OTUs/ASVs, columns = samples. Used to compute module eigengenes or module abundance. Must align with graph_obj node names (rownames) and env sample IDs.

env_select

Named list. Column indices or names for each env block. Each block corresponds to one heatmap quadrant. E.g. list(Env01 = 1:5, Env02 = 6:10, Env03 = 11:15, Env04 = 16:20).

module_index

Character. How to represent each module for env correlation: "eigengene" (default, PC1 of module OTUs) or "abundance" (sum/mean of module OTU abundances).

abundance_type

Character. When module_index = "abundance", use "sum" or "mean".

relation_method

"correlation" or "mantel".

cor.method

Correlation method: "pearson", "kendall", "spearman".

cor.use

Handling of missing values in correlation.

mantel.method2

Correlation for Mantel test.

drop_nonsig

Logical. Drop non-significant links from plot.

layout

Character. Layout for ggNetView (e.g. "gephi", "square").

layout.module

Character. Module ordering strategy passed through to the underlying ggNetView call. One of "random" (default), "adjacent" or "order".

orientation

Character vector. Heatmap quadrants: "top_right", "bottom_right", "top_left", "bottom_left".

distance

Numeric. Gap between the scaled network boundary and the environmental heatmaps.

r

Numeric. Effective radius for scaling the central network.

HeatmapScale

Numeric (default = 1). Global scale factor for the overall heatmap size. Values > 1 enlarge the whole heatmap layout.

SigLineAlpha

Numeric (default = 0.5). Transparency for module-heatmap link lines. Must be between 0 and 1.

HeatmapLabelSize

Numeric (default = 5). Text size for the heatmap row/column labels.

HeatmapSigSize

Numeric (default = 5). Text size for the significance marks rendered on the heatmap tiles.

HeatmapColorBar

A list of length-2 character vectors giving (low, high) hex colours, one per heatmap quadrant. NULL (default) uses the package colour palette.

HeatmapLabelOrient

Numeric (default = 0). Rotation in degrees applied to the heatmap labels.

SigLineWidth

Numeric vector of length 2 (default = c(0.5, 2)). Min and max line width for module-heatmap links. Line width is mapped from -log10(p-value): smaller p (more significant) -> thicker line. E.g. p=0.05->1.3, p=0.01->2, p=0.001->3; values are scaled to this range.

SigLineColor

Character vector of length 2. Colors for link gradient (low and high correlation).

HeatmapPointSize

Numeric (default = 5). Point size for the central module anchor used to attach the heatmap.

HeatmapPointFill

Character (default = "#de77ae"). Fill colour for the central module anchor point.

HeatmapTileColor

Border colour for the heatmap tiles. Default NA (no border).

HeatmapTileSize

Numeric (default = 0). Border size for the heatmap tiles.

...

Additional arguments passed to layout and network rendering, including: layout, layout.module, shrink, jitter, add_outer, add_group_outer, label (logical or character: module labels in ggNetView style), labelsize, labelsegmentsize, labelsegmentalpha, fill, color, pointsize.

Value

A list: [[1]] ggplot with straight links, [[2]] ggplot with curved links, [[3]] data frame of module-env correlation stats.