10 Network & Environment
Load R Package
library(tidyverse) # data manipulation / piping utilities
library(ggNetView) # graph builders + info-extraction helpersExample data
# Built-in example datasets shipped with ggNetView:
# `Envdf_4st` - environmental table (samples x env variables)
# `Spedf` - species/feature table (samples x species)
# Row order MUST match between the two tables.
data("Envdf_4st")
data("Spedf")10.1 Network Environment (one core with 4 Envrionment matrix)
# ---- Plot: 1 central species block + 4 environmental heatmap quadrants ----
# `relation_method = "correlation"` means spec-env links are based on
# correlations (psych::corr.test) rather than community distance / mantel.
out1 <- gglink_heatmaps(
env = Envdf_4st, # environmental table: rows = samples, cols = env factors
spec = Spedf, # species table: rows = samples (same order as env), cols = species
env_select = list( # one heatmap quadrant per env block (length must match `orientation`)
Env01 = 1:14,
Env02 = 15:28,
Env03 = 29:42,
Env04 = 43:56
),
spec_select = list( # one central species network per block
Spec01 = 1:8 # take species columns 1..8
),
relation_method = "correlation", # spec-env link rule: "correlation" (vs "mantel" / "vegdist")
spec_layout = "circle_outline", # shape of the central network: nodes on a circle outline
cor.method = "pearson", # correlation method used for env-env tiles and spec-env links
cor.use = "pairwise", # NA handling: use pairwise-complete observations
r = 6, # effective radius of the central network
distance = 1, # offset between the central network and each surrounding heatmap
HeatmapLabelOrient = 45, # rotate heatmap row/column labels 45 deg to avoid overlap
HeatmapLabelSize = 3, # smaller label font (3) since many labels are crammed at 45 deg
orientation = c( # which quadrant each env block lands in (paired with `env_select` in order)
"top_right",
"bottom_right",
"top_left",
"bottom_left"
)
)## The max module in network is 2 we use the 2 modules for next analysis
class(out1)## [1] "list"
length(out1)## [1] 3
out1[[1]] # gglink_heatmaps() returns a list of ggplot variants; [[1]] = the default view
out1[[2]] # the 2nd ggplot variant (different style — legend / annotation layer)
head(out1[[3]])## ID Type Correlation Pvalue p_signif spec_block env_block
## 1 Callvulg N_1 0.194775914 0.36174639 Spec01 Env01
## 2 Callvulg P_1 -0.089825004 0.67638229 Spec01 Env01
## 3 Callvulg K_1 0.508915172 0.01109495 * Spec01 Env01
## 4 Callvulg Ca_1 0.004323521 0.98400337 Spec01 Env01
## 5 Callvulg Mg_1 0.114475972 0.59428736 Spec01 Env01
## 6 Callvulg S_1 0.401157542 0.05203489 Spec01 Env01
## method
## 1 correlation
## 2 correlation
## 3 correlation
## 4 correlation
## 5 correlation
## 6 correlation10.2 Network Environment (one core with 3 Environment matrix)
# ---- Plot: 1 central species block + 3 environmental heatmap quadrants ----
# Like the 4-quadrant version, but with Env02 dropped and custom styling:
# - drop_nonsig = TRUE : hide non-significant spec-env links
# - HeatmapColorBar : custom low/high colour pair per quadrant
# - HeatmapPointFill / CorePointFill : override default fill colours
out2 <- gglink_heatmaps(
env = Envdf_4st, # environmental table: rows = samples, cols = env factors
spec = Spedf, # species table: rows = samples (same order as env), cols = species
env_select = list( # 3 env blocks -> 3 heatmap quadrants
Env01 = 1:14,
Env03 = 29:40,
Env04 = 43:50
),
spec_select = list(Spec01 = 1:8), # one central species network (species cols 1..8)
relation_method = "correlation", # spec-env link rule: correlation (vs "mantel" / "vegdist")
spec_layout = "circle_outline", # shape of the central network: nodes on a circle outline
cor.method = "pearson", # correlation method for env-env tiles and spec-env links
cor.use = "pairwise", # NA handling: pairwise-complete observations
drop_nonsig = TRUE, # remove non-significant spec-env links from the plot (still kept in stats)
HeatmapColorBar = list( # one low/high colour pair per env block (length = 3)
c("#2166ac", "#b2182b"), # quadrant 1: blue -> red
c("#1b7837", "#762a83"), # quadrant 2: green -> purple
c("#4393c3", "#d6604d") # quadrant 3: light blue -> brick
),
HeatmapPointFill = "#8c6bb1", # fill of the diagonal anchor points on each heatmap
CorePointFill = "#225ea8", # fill of the central species nodes
HeatmapLabelOrient = 45, # rotate heatmap labels 45 deg to avoid overlap
HeatmapLabelSize = 3, # smaller label font (3) since many labels are crammed at 45 deg
r = 6, # effective radius of the central network
distance = 1, # offset between the central network and each surrounding heatmap
orientation = c( # 3 quadrants — length MUST match `env_select`
"top_right",
"top_left",
"bottom_left"
)
)## The max module in network is 2 we use the 2 modules for next analysis
out2[[1]] # default view (1st ggplot variant from the returned list)
out2[[1]] # NOTE: duplicate of the line above — same plot; can be removed
head(out2[[3]]) # the 3rd ggplot variant (different style/annotation)## ID Type Correlation Pvalue p_signif spec_block env_block
## 1 Callvulg N_1 0.194775914 0.36174639 Spec01 Env01
## 2 Callvulg P_1 -0.089825004 0.67638229 Spec01 Env01
## 3 Callvulg K_1 0.508915172 0.01109495 * Spec01 Env01
## 4 Callvulg Ca_1 0.004323521 0.98400337 Spec01 Env01
## 5 Callvulg Mg_1 0.114475972 0.59428736 Spec01 Env01
## 6 Callvulg S_1 0.401157542 0.05203489 Spec01 Env01
## method
## 1 correlation
## 2 correlation
## 3 correlation
## 4 correlation
## 5 correlation
## 6 correlation10.3 Network Environment (one core with 4 Envrionment matrix)
# ---- Plot: 1 central species block + 4 environmental heatmap quadrants ----
# `gglink_heatmaps()` puts a central species network in the middle, surrounds
# it with one env-env heatmap per "quadrant", and draws spec-env correlation
# links between the central nodes and the diagonal anchor points on each heatmap.
p0 <- gglink_heatmaps(
env = Envdf_4st, # environmental table: rows = samples, cols = env factors
spec = Spedf, # species table: rows = samples (same order as env), cols = species
spec_select = list( # one central species network per block
Spec01 = 1:15 # take species columns 1..15
),
env_select = list( # one heatmap quadrant per env block (length must match `orientation`)
Env01 = 1:14,
Env02 = 15:28,
Env03 = 29:42,
Env04 = 43:56
),
orientation = c( # where each env block is drawn relative to the centre
"top_right",
"bottom_right",
"top_left",
"bottom_left"
),
cor.method = "pearson", # correlation method (Pearson / Spearman / Kendall)
cor.use = "pairwise", # NA handling: pairwise-complete observations
distance = 0.5, # offset between central network and the heatmaps (bigger = pushed out further)
drop_nonsig = T, # hide non-significant spec-env links (still kept in the stats data)
r = 4, # effective radius of the central network
scale_networks = T, # normalise each central network to the same visual radius
group_layout = "snake", # anchor arrangement for multi-block centres (here only 1 block, so cosmetic)
spec_layout = "square_outline", # shape of the central network: nodes on a circle outline
anchor_dist = 13, # spacing between anchors
HeatmapLabelSize = 4, # font size of row/column labels on heatmaps
HeatmapSigSize = 5, # font size of significance marks (*, **, ***) inside heatmap tiles
HeatmapColorBar = list( # one low/high colour pair per heatmap quadrant (length = # of env blocks)
c("#2166ac", "#b2182b"), # quadrant 1: blue -> red
c("#1b7837", "#762a83"), # quadrant 2: green -> purple
c("#4393c3", "#d6604d"), # quadrant 3: light blue -> brick
c("#92c5de", "#f4a582") # quadrant 4: pale blue -> peach
),
HeatmapLabelOrient = 45, # rotation angle (deg) for heatmap labels — 45 avoids overlap
SigLineWidth = c(1, 5), # min/max line width for SIGNIFICANT spec-env links (mapped by strength)
SigLineColor = c("#9ecae1", "#fc9272"), # colour gradient endpoints for significant links (low -> high)
HeatmapPointSize = 5, # size of the diagonal anchor points where links land on each heatmap
CorePointSize = 10, # size of the central species nodes
HeatmapPointFill = "#3690c0", # fill colour of the heatmap diagonal anchor points
CorePointFill = "#e7298a" # fill colour of the central species nodes
)## The max module in network is 3 we use the 3 modules for next analysis
p0[[1]] # gglink_heatmaps() returns a list of ggplot variants; [[1]] = the default view
10.4 Network Environment (two core)
# ---- Plot: 2 central species blocks, each with its own layout shape ----
# `spec_select` now has 2 entries -> 2 central networks placed on the anchor frame.
# `spec_layout` gives one shape per block: first block circular outline, second square.
p <- gglink_heatmaps(
env = Envdf_4st,
spec = Spedf,
spec_select = list(
Spec01 = 1:15, # block 1: species cols 1..15
Spec02 = 1:15 # block 2: same cols (demo; in real use pick a different set)
),
env_select = list(
Env01 = 1:14,
Env02 = 15:28,
Env03 = 29:42,
Env04 = 43:56
),
spec_layout = c("circle_outline", "square_outline"), # one layout shape per spec block
orientation = c(
"top_right",
"bottom_right",
"top_left",
"bottom_left"
),
cor.method = "pearson",
cor.use = "pairwise",
distance = 0.5,
drop_nonsig = T,
r = 4,
scale_networks = T,
group_layout = "snake", # anchor arrangement for the 2 central networks
anchor_dist = 13,
HeatmapLabelSize = 4,
HeatmapSigSize = 5,
HeatmapColorBar = list(
c("#2166ac", "#b2182b"),
c("#1b7837", "#762a83"),
c("#4393c3", "#d6604d"),
c("#92c5de", "#f4a582")
),
HeatmapLabelOrient = 45,
SigLineWidth = c(1, 5),
SigLineColor = c("#9ecae1", "#fc9272"),
HeatmapPointSize = 5,
CorePointSize = 10,
HeatmapPointFill = "#3690c0",
CorePointFill = "#e7298a"
)## The max module in network is 3 we use the 3 modules for next analysis
## The max module in network is 3 we use the 3 modules for next analysis
p[[2]] # take the 2nd element from the return list (different ggplot variant)
10.5 Network Environment (three core)
# ---- Plot 2: THREE central species blocks + restricted spec-env comparisons ----
# - 3 spec blocks, each with a different layout shape.
# - `comparisons_groups` restricts which (env_block, spec_block) pairs get linked
# instead of drawing every possible combination.
# - `scale_networks = FALSE` lets the 3 blocks keep their native sizes.
p2 <- gglink_heatmaps(
env = Envdf_4st,
spec = Spedf,
spec_select = list(
Spec01 = 1:15,
Spec02 = 1:15,
Spec03 = 16:20 # smaller 3rd block to demo size differences
),
env_select = list(
Env01 = 1:14,
Env02 = 15:28,
Env03 = 29:42,
Env04 = 43:56
),
orientation = c(
"top_right",
"bottom_right",
"top_left",
"bottom_left"
),
spec_layout = c("rectangle_outline", "square_outline", "circle_outline"), # one shape per spec block
cor.method = "pearson",
cor.use = "pairwise",
distance = 1, # bigger gap between centre and heatmaps
drop_nonsig = T,
r = 1.2, # minimum block radius (because scale_networks = F, this is the floor)
scale_networks = F, # do NOT normalise sizes -> blocks keep their natural scale
anchor_dist = 6,
HeatmapLabelSize = 4,
HeatmapSigSize = 5,
HeatmapColorBar = list(
c("#2166ac", "#b2182b"),
c("#1b7837", "#762a83"),
c("#4393c3", "#d6604d"),
c("#92c5de", "#f4a582")
),
HeatmapLabelOrient = 45,
SigLineWidth = c(1, 5),
SigLineColor = c("#9ecae1", "#fc9272"),
comparisons = T, # master switch: enable spec-env analysis + linking
comparisons_groups = list( # only draw links for these specific (env_block, spec_block) pairs
c("Env01", "Spec01"),
c("Env02", "Spec02"),
c("Env03", "Spec03"),
c("Env04", "Spec03")
),
HeatmapPointSize = 5,
CorePointSize = 10,
HeatmapPointFill = "#3690c0",
CorePointFill = "#e7298a"
)## The max module in network is 3 we use the 3 modules for next analysis
## The max module in network is 3 we use the 3 modules for next analysis## The max module in network is 2 we use the 2 modules for next analysis
p2[[1]]
10.6 Mantel test and drop_nonsig = T
p2 <- gglink_heatmaps(
# ---- Data input ----
env = Envdf_4st, # environmental data frame: one column per env variable
spec = Spedf, # species data frame: one column per species / taxonomic unit
# ---- Spec blocks (central networks) ----
# Each list element defines one central species network (column indices into `spec`).
# The block names (Spec01, Spec02 ...) are used later to match `comparisons_groups`.
# NOTE: spec_collapse = TRUE is enabled below, so these 10 blocks are NOT drawn as
# networks — each one is collapsed into a single labelled point bearing the block name.
spec_select = list(Spec01 = 1:15,
Spec02 = 1:15,
Spec03 = 16:20,
Spec04 = 16:20,
Spec05 = 16:20,
Spec06 = 16:20,
Spec07 = 5:20,
Spec08 = 21:25,
Spec09 = 26:35,
Spec10 = 36:44
),
# ---- Collapse each spec_block into a single point ----
# T = each spec_select element is rendered as ONE labelled point ("Spec01"..."Spec10").
# In this mode spec_layout / spec_relation / scale_networks have no effect (no network drawn).
# The point positions are decided by `group_layout` below.
spec_collapse = T,
# ---- Env blocks (the four heatmap quadrants) ----
# Each element defines one env block; each block becomes one heatmap quadrant.
env_select = list(Env01 = 1:14,
Env02 = 15:28,
Env03 = 29:42,
Env04 = 43:56),
# ---- Orientation of the four heatmaps ----
# Order pairs with env_select: Env01 -> top_right, Env02 -> bottom_right, etc.
orientation = c("top_right",
"bottom_right",
"top_left",
"bottom_left"),
# spec_layout = c("rectangle_outline", "square_outline", "circle_outline"),
# ^ Node-shape layout for the central species networks; ignored when spec_collapse = T,
# so commenting it out makes no difference here.
# ---- Relation method (this run uses mantel) ----
relation_method = "mantel", # use the mantel branch instead of correlation
mantel.method = "mantel", # legacy compatibility argument; unused by the current implementation, leave as-is
mantel_kind = c("col_vs_col"), # * mantel granularity:
# "col_vs_col" = legacy mode: spec single-column dist
# vs env single-column dist (close to rank correlation)
# "block_vs_col" = recommended ecological mode (default):
# spec WHOLE-BLOCK dist vs single env column dist
# NOTE: under col_vs_col + spec_collapse = T, every link generated
# by each spec column inside a block starts from the SAME
# collapsed point — a console message will warn about this.
cor.method = "pearson", # correlation method; under mantel mode it falls through to mantel.method2; also used for env-env autocorrelation heatmaps
cor.use = "pairwise", # NA handling: pairwise-complete observations
drop_nonsig = T, # T = hide non-significant links from the plot
# ---- Central-network geometry ----
r = 1, # base radius of the central network; under spec_collapse = T only controls how tightly the points pack
scale_networks = F, # F = do NOT normalise all networks to a common size;
# auto-disabled when spec_collapse = T
# ---- Overall arrangement of the (collapsed) spec points ----
group_layout = "circle", # ring layout: the 10 points are spread evenly around a circle
# nrow = 5, # only used by row/column/snake layouts; no effect for circle
anchor_dist = 8, # distance from each point to the centre (radius of the ring)
distance = 4, # offset between the centre point group and the outer heatmaps
# ---- Heatmap text annotations ----
HeatmapLabelSize = 4, # font size for heatmap row/col labels (ID/Type)
HeatmapSigSize = 5, # font size for the significance marks (*, **, ***) inside heatmap tiles
# ---- Per-quadrant colour palettes (low -> high) ----
# Length must match `orientation` (4 quadrants); paired in order.
HeatmapColorBar = list(
c("#2166ac", "#b2182b"), # quadrant 1: top_right
c("#1b7837", "#762a83"), # quadrant 2: bottom_right
c("#4393c3", "#d6604d"), # quadrant 3: top_left
c("#92c5de", "#f4a582") # quadrant 4: bottom_left
),
HeatmapLabelOrient = 45, # rotate heatmap labels 45 deg to avoid overlap
# ---- Spec-env link (segment) styling ----
SigLineWidth = c(1, 5), # min / max line width for significant links (mapped by -log10(p))
SigLineColor = c("#9ecae1", "#fc9272"), # colour gradient endpoints for mantel r low / high
# ---- Restrict which (env_block, spec_block) pairs are drawn ----
# Under mantel mode, each (env_block, spec_block) pair triggers a set of mantel tests
# (col_vs_col: |spec cols| x |env cols| tests; block_vs_col: |env cols| tests).
comparisons = T, # enable the restriction (otherwise ALL possible pairs are drawn)
comparisons_groups = list(
c("Env01", "Spec01"), # Env01 paired only with Spec01
c("Env02", "Spec02"), # Env02 paired only with Spec02
c("Env03", "Spec03"), # Env03 paired only with Spec03
c("Env04", "Spec03") # Env04 also paired only with Spec03
),
# ---- Point sizes ----
HeatmapPointSize = 4, # size of the anchor points on each heatmap's diagonal
CorePointSize = 10, # size of the collapsed spec points (larger than non-collapse default for visibility)
# ---- Point fill colours (vectors are recycled in order) ----
# HeatmapPointFill: length = # of quadrants (4), paired with `orientation` in order.
HeatmapPointFill = c("#2166ac", "#b2182b", "#1b7837", "#762a83"),
# CorePointFill: length = # of spec_select blocks (10), paired with names(spec_select) in order.
# With spec_collapse = T, each block is one point, so 1 colour = 1 point.
# First 5 points blue, last 5 points red — visually splits the 10 blocks into two groups.
CorePointFill = c("#2166ac", "#2166ac", "#2166ac", "#2166ac",
"#2166ac", "#b2182b", "#b2182b", "#b2182b",
"#b2182b", "#b2182b")
)## `spec_collapse = TRUE` collapses each spec block into one point; in the current mode (relation_method = 'mantel', mantel_kind = 'col_vs_col') link sources are per spec column, so all column-level links from a block will originate from the same collapsed point. Consider `relation_method = 'mantel'` + `mantel_kind = 'block_vs_col'` for a one-line-per-block visualisation.
p2[[2]] # curved-line connection version
head(p2[[3]])## ID Type Correlation Pvalue spec_block env_block p_signif method
## 1 Callvulg N_1 0.01289455 0.382 Spec01 Env01 mantel
## 2 Empenigr N_1 0.01959886 0.350 Spec01 Env01 mantel
## 3 Rhodtome N_1 -0.15248826 0.893 Spec01 Env01 mantel
## 4 Vaccmyrt N_1 -0.02514002 0.528 Spec01 Env01 mantel
## 5 Vaccviti N_1 0.07366673 0.230 Spec01 Env01 mantel
## 6 Pinusylv N_1 0.12714109 0.161 Spec01 Env01 mantel10.7 Network Environment (multi-core)
p2 <- gglink_heatmaps(
# ---- Data input ----
env = Envdf_4st, # environmental data frame: one column per env variable
spec = Spedf, # species data frame: one column per species / taxonomic unit
# ---- Spec blocks (central networks) ----
# Each list element defines one central species network (column indices into `spec`).
# The block names (Spec01, Spec02 ...) are used later to match `comparisons_groups`.
spec_select = list(Spec01 = 1:15,
Spec02 = 1:15,
Spec03 = 16:20,
Spec04 = 16:20,
Spec05 = 16:20,
Spec06 = 16:20,
Spec07 = 5:20,
Spec08 = 21:25,
Spec09 = 26:35,
Spec10 = 36:44),
# ---- Env blocks (the four heatmap quadrants) ----
# Each element defines one env block; each block becomes one heatmap quadrant.
env_select = list(Env01 = 1:14,
Env02 = 15:28,
Env03 = 29:42,
Env04 = 43:56),
# ---- Orientation of the four heatmaps ----
# Order pairs with env_select: Env01 -> top_right, Env02 -> bottom_right, etc.
orientation = c("top_right",
"bottom_right",
"top_left",
"bottom_left"),
# spec_layout = c("rectangle_outline", "square_outline", "circle_outline"),
# ^ Node-shape layout for the central species networks; commented out here, so the default "circle_outline" is used.
# ---- Correlation parameters ----
cor.method = "pearson", # correlation method: pearson / kendall / spearman
cor.use = "pairwise", # NA handling: pairwise-complete observations
drop_nonsig = T, # T = hide non-significant links from the plot
# ---- Central-network geometry ----
r = 1, # base radius of the central network
scale_networks = F, # F = do NOT normalise all networks to a common size;
# networks with more nodes will be scaled up proportionally
# ---- Overall arrangement of the multiple spec networks ----
group_layout = "snake", # snake layout (rows zig-zag back and forth)
nrow = 5, # number of rows used by the snake layout (10 networks -> 5 rows x 2 cols)
anchor_dist = 8, # spacing between adjacent central networks
distance = 6, # offset between the central networks and the outer heatmaps
# ---- Heatmap text annotations ----
HeatmapLabelSize = 4, # font size for heatmap row/col labels (ID/Type)
HeatmapSigSize = 5, # font size for the significance marks (*, **, ***) inside heatmap tiles
# ---- Per-quadrant colour palettes (low -> high) ----
# Length must match `orientation` (4 quadrants); paired in order.
HeatmapColorBar = list(
c("#2166ac", "#b2182b"), # quadrant 1: top_right
c("#1b7837", "#762a83"), # quadrant 2: bottom_right
c("#4393c3", "#d6604d"), # quadrant 3: top_left
c("#92c5de", "#f4a582") # quadrant 4: bottom_left
),
HeatmapLabelOrient = 45, # rotate heatmap labels 45 deg to avoid overlap
# ---- Spec-env link (segment) styling ----
SigLineWidth = c(1, 5), # min / max line width for the links (mapped by -log10(p))
SigLineColor = c("#9ecae1", "#fc9272"), # colour gradient endpoints for correlation low / high
# ---- Restrict which (env_block, spec_block) pairs are drawn ----
comparisons = T, # enable the restriction (otherwise ALL possible pairs are drawn)
comparisons_groups = list(
c("Env01", "Spec01"), # Env01 paired only with Spec01
c("Env02", "Spec02"), # Env02 paired only with Spec02
c("Env03", "Spec03"), # Env03 paired only with Spec03
c("Env04", "Spec03") # Env04 also paired only with Spec03
),
# ---- Point sizes ----
HeatmapPointSize = 5, # size of the anchor points on each heatmap's diagonal
CorePointSize = 5, # size of the central-network nodes
# ---- Point fill colours (vectors are recycled in order) ----
# HeatmapPointFill: length = # of quadrants (4), paired with `orientation` in order.
HeatmapPointFill = c("#2166ac", "#b2182b", "#1b7837", "#762a83"),
# CorePointFill: length = # of spec_select blocks (10), paired with names(spec_select) in order.
# First 5 networks coloured blue, last 5 coloured red — visually splits the 10 networks into two groups.
CorePointFill = c("#2166ac", "#2166ac", "#2166ac", "#2166ac",
"#2166ac", "#b2182b", "#b2182b", "#b2182b",
"#b2182b", "#b2182b")
)## The max module in network is 3 we use the 3 modules for next analysis
## The max module in network is 3 we use the 3 modules for next analysis## The max module in network is 2 we use the 2 modules for next analysis
## The max module in network is 2 we use the 2 modules for next analysis
## The max module in network is 2 we use the 2 modules for next analysis
## The max module in network is 2 we use the 2 modules for next analysis## The max module in network is 3 we use the 3 modules for next analysis## The max module in network is 2 we use the 2 modules for next analysis
## The max module in network is 2 we use the 2 modules for next analysis## The max module in network is 3 we use the 3 modules for next analysis
p2[[1]] # take the 1st element: the straight-line version of the plot
10.8 Network Environment (combine-core to one point)
p2 <- gglink_heatmaps(
# ---- Data input ----
env = Envdf_4st, # environmental data frame: one column per env variable
spec = Spedf, # species data frame: one column per species / taxonomic unit
# ---- Spec blocks (central networks) ----
# Each list element defines one central species network (column indices into `spec`).
# The block names (Spec01, Spec02 ...) are used later to match `comparisons_groups`.
# NOTE: spec_collapse = TRUE is enabled below, so these 6 blocks are NOT drawn as
# networks — each one is collapsed into a single labelled point bearing the block name.
spec_select = list(Spec01 = 1:10,
Spec02 = 11:20,
Spec03 = 5:21,
Spec04 = 20:26,
Spec05 = 30:40,
Spec06 = 25:44),
# ---- Collapse each spec_block into a single point ----
# T = each spec_select element is rendered as ONE labelled point ("Spec01"..."Spec06").
# In this mode spec_layout / spec_relation / scale_networks have no effect (no network drawn).
# The point positions are decided by `group_layout` below.
spec_collapse = T,
# ---- Env blocks (the four heatmap quadrants) ----
# Each element defines one env block; each block becomes one heatmap quadrant.
env_select = list(Env01 = 1:14,
Env02 = 15:28,
Env03 = 29:42,
Env04 = 43:56),
# ---- Orientation of the four heatmaps ----
# Order pairs with env_select: Env01 -> top_right, Env02 -> bottom_right, etc.
orientation = c("top_right",
"bottom_right",
"top_left",
"bottom_left"),
# spec_layout = c("rectangle_outline", "square_outline", "circle_outline"),
# ^ Node-shape layout for the central species networks; ignored when spec_collapse = T,
# so commenting it out makes no difference here.
# ---- Relation method (this run uses mantel) ----
relation_method = "mantel", # use the mantel branch instead of correlation
mantel.method = "mantel", # legacy compatibility argument; unused by the current implementation, leave as-is
mantel_kind = c("col_vs_col"), # * mantel granularity:
# "col_vs_col" = legacy mode: spec single-column dist
# vs env single-column dist (close to rank correlation)
# "block_vs_col" = recommended ecological mode (default):
# spec WHOLE-BLOCK dist vs single env column dist
# NOTE: under col_vs_col + spec_collapse = T, every link generated
# by each spec column inside a block starts from the SAME
# collapsed point — a console message will warn about this.
cor.method = "pearson", # correlation method; under mantel mode it falls through to mantel.method2; also used for env-env autocorrelation heatmaps
cor.use = "pairwise", # NA handling: pairwise-complete observations
drop_nonsig = T, # T = hide non-significant links from the plot
# ---- Central-network geometry ----
r = 0.1, # base radius of the central network; under spec_collapse = T only controls how tightly the points pack
scale_networks = F, # F = do NOT normalise all networks to a common size;
# auto-disabled when spec_collapse = T
# ---- Overall arrangement of the (collapsed) spec points ----
group_layout = "row", # row layout: points are placed along a horizontal row
group_angle = 45, # rotate the whole point row by 45 deg around the centre
# nrow = 5, # only used by row/column/snake when wrapping into multiple rows; not needed here
anchor_dist = 4, # spacing between adjacent points along the row
distance = -3, # offset between the centre point group and the outer heatmaps (negative -> pull heatmaps INWARD, toward the centre)
# ---- Heatmap text annotations ----
HeatmapLabelSize = 4, # font size for heatmap row/col labels (ID/Type)
HeatmapSigSize = 5, # font size for the significance marks (*, **, ***) inside heatmap tiles
# ---- Per-quadrant colour palettes (low -> high) ----
# Length must match `orientation` (4 quadrants); paired in order.
HeatmapColorBar = list(
c("#2166ac", "#b2182b"), # quadrant 1: top_right
c("#1b7837", "#762a83"), # quadrant 2: bottom_right
c("#4393c3", "#d6604d"), # quadrant 3: top_left
c("#92c5de", "#f4a582") # quadrant 4: bottom_left
),
HeatmapLabelOrient = 45, # rotate heatmap labels 45 deg to avoid overlap
# ---- Spec-env link (segment) styling ----
SigLineWidth = c(1, 5), # min / max line width for the links (mapped by -log10(p))
SigLineColor = c("#9ecae1", "#fc9272"), # colour gradient endpoints for mantel r low / high
# ---- Restrict which (env_block, spec_block) pairs are drawn ----
# Under mantel mode, each (env_block, spec_block) pair triggers a set of mantel tests
# (col_vs_col: |spec cols| x |env cols| tests; block_vs_col: |env cols| tests).
comparisons = T, # enable the restriction (otherwise ALL possible pairs are drawn)
comparisons_groups = list(
c("Env01", "Spec01"), # Env01 paired only with Spec01
c("Env02", "Spec02"), # Env02 paired only with Spec02
c("Env03", "Spec03"), # Env03 paired only with Spec03
c("Env04", "Spec03") # Env04 also paired only with Spec03
),
# ---- Point sizes ----
HeatmapPointSize = 4, # size of the anchor points on each heatmap's diagonal
CorePointSize = 10, # size of the collapsed spec points (larger than non-collapse default for visibility)
# ---- Point fill colours (vectors are recycled in order) ----
# HeatmapPointFill: length = # of quadrants (4), paired with `orientation` in order.
HeatmapPointFill = c("#2166ac", "#b2182b", "#1b7837", "#762a83"),
# CorePointFill: length = # of spec_select blocks (6), paired with names(spec_select) in order.
# With spec_collapse = T, each block is one point, so 1 colour = 1 point.
# Six distinct colours here, one per Spec01..Spec06 — visually distinguishes every block.
CorePointFill = c("#2166ac", "#b2182b", "#1b7837",
"#762a83", "#9ecae1", "#fc9272")
)## `spec_collapse = TRUE` collapses each spec block into one point; in the current mode (relation_method = 'mantel', mantel_kind = 'col_vs_col') link sources are per spec column, so all column-level links from a block will originate from the same collapsed point. Consider `relation_method = 'mantel'` + `mantel_kind = 'block_vs_col'` for a one-line-per-block visualisation.## `distance = -3` is negative; the env heatmaps will be pulled inward and may overlap the central point group. If a heatmap anchor becomes <= 0 you will get a warning and the corresponding heatmap may flip to the opposite side -- use a less negative value if that happens.
p2[[1]]
10.9 Change group angle
p3 <- gglink_heatmaps(
# ---- Data input ----
env = Envdf_4st, # environmental data frame: one column per env variable
spec = Spedf, # species data frame: one column per species / taxonomic unit
# ---- Spec blocks (central networks) ----
# Each list element defines one central species network (column indices into `spec`).
# The block names (Spec01, Spec02 ...) are used later to match `comparisons_groups`.
# NOTE: spec_collapse = TRUE is enabled below, so these 6 blocks are NOT drawn as
# networks — each one is collapsed into a single labelled point bearing the block name.
spec_select = list(Spec01 = 1:10,
Spec02 = 11:20,
Spec03 = 5:21,
Spec04 = 20:26,
Spec05 = 30:40,
Spec06 = 25:44),
# ---- Collapse each spec_block into a single point ----
# T = each spec_select element is rendered as ONE labelled point ("Spec01"..."Spec06").
# In this mode spec_layout / spec_relation / scale_networks have no effect (no network drawn).
# The point positions are decided by `group_layout` below.
spec_collapse = T,
# ---- Env blocks (the four heatmap quadrants) ----
# Each element defines one env block; each block becomes one heatmap quadrant.
env_select = list(Env01 = 1:14,
Env02 = 15:28,
Env03 = 29:42,
Env04 = 43:56),
# ---- Orientation of the four heatmaps ----
# Order pairs with env_select: Env01 -> top_right, Env02 -> bottom_right, etc.
orientation = c("top_right",
"bottom_right",
"top_left",
"bottom_left"),
# spec_layout = c("rectangle_outline", "square_outline", "circle_outline"),
# ^ Node-shape layout for the central species networks; ignored when spec_collapse = T,
# so commenting it out makes no difference here.
# ---- Relation method (this run uses mantel) ----
relation_method = "mantel", # use the mantel branch instead of correlation
mantel.method = "mantel", # legacy compatibility argument; unused by the current implementation, leave as-is
mantel_kind = c("col_vs_col"), # * mantel granularity:
# "col_vs_col" = legacy mode: spec single-column dist
# vs env single-column dist (close to rank correlation)
# "block_vs_col" = recommended ecological mode (default):
# spec WHOLE-BLOCK dist vs single env column dist
# NOTE: under col_vs_col + spec_collapse = T, every link generated
# by each spec column inside a block starts from the SAME
# collapsed point — a console message will warn about this.
cor.method = "pearson", # correlation method; under mantel mode it falls through to mantel.method2; also used for env-env autocorrelation heatmaps
cor.use = "pairwise", # NA handling: pairwise-complete observations
drop_nonsig = T, # T = hide non-significant links from the plot
# ---- Central-network geometry ----
r = 0.1, # base radius of the central network; under spec_collapse = T only controls how tightly the points pack
scale_networks = F, # F = do NOT normalise all networks to a common size;
# auto-disabled when spec_collapse = T
# ---- Overall arrangement of the (collapsed) spec points ----
group_layout = "arc", # arc layout: points are spread along an ARC (a partial circle, not a full ring)
group_angle = 45, # rotate the whole arc by 45 deg around the centre (starting angle)
group_arc_angle = 90, # angular span of the arc in degrees: 90 = quarter circle, 180 = half circle, 360 = full ring
# nrow = 5, # only used by row/column/snake when wrapping into multiple rows; not needed here
anchor_dist = 4, # distance from each point to the centre (radius of the arc)
distance = -3, # offset between the centre point group and the outer heatmaps (negative -> pull heatmaps INWARD, toward the centre)
# ---- Heatmap text annotations ----
HeatmapLabelSize = 4, # font size for heatmap row/col labels (ID/Type)
HeatmapSigSize = 5, # font size for the significance marks (*, **, ***) inside heatmap tiles
# ---- Per-quadrant colour palettes (low -> high) ----
# Length must match `orientation` (4 quadrants); paired in order.
HeatmapColorBar = list(
c("#2166ac", "#b2182b"), # quadrant 1: top_right
c("#1b7837", "#762a83"), # quadrant 2: bottom_right
c("#4393c3", "#d6604d"), # quadrant 3: top_left
c("#92c5de", "#f4a582") # quadrant 4: bottom_left
),
HeatmapLabelOrient = 45, # rotate heatmap labels 45 deg to avoid overlap
# ---- Spec-env link (segment) styling ----
SigLineWidth = c(1, 5), # min / max line width for the links (mapped by -log10(p))
SigLineColor = c("#9ecae1", "#fc9272"), # colour gradient endpoints for mantel r low / high
# ---- Restrict which (env_block, spec_block) pairs are drawn ----
# Under mantel mode, each (env_block, spec_block) pair triggers a set of mantel tests
# (col_vs_col: |spec cols| x |env cols| tests; block_vs_col: |env cols| tests).
comparisons = T, # enable the restriction (otherwise ALL possible pairs are drawn)
comparisons_groups = list(
c("Env01", "Spec01"), # Env01 paired only with Spec01
c("Env02", "Spec02"), # Env02 paired only with Spec02
c("Env03", "Spec03"), # Env03 paired only with Spec03
c("Env04", "Spec03") # Env04 also paired only with Spec03
),
# ---- Point sizes ----
HeatmapPointSize = 4, # size of the anchor points on each heatmap's diagonal
CorePointSize = 10, # size of the collapsed spec points (larger than non-collapse default for visibility)
# ---- Point fill colours (vectors are recycled in order) ----
# HeatmapPointFill: length = # of quadrants (4), paired with `orientation` in order.
HeatmapPointFill = c("#2166ac", "#b2182b", "#1b7837", "#762a83"),
# CorePointFill: length = # of spec_select blocks (6), paired with names(spec_select) in order.
# With spec_collapse = T, each block is one point, so 1 colour = 1 point.
# Six distinct colours, one per Spec01..Spec06 — visually distinguishes every block.
CorePointFill = c("#2166ac", "#b2182b", "#1b7837",
"#762a83", "#9ecae1", "#fc9272")
)## `spec_collapse = TRUE` collapses each spec block into one point; in the current mode (relation_method = 'mantel', mantel_kind = 'col_vs_col') link sources are per spec column, so all column-level links from a block will originate from the same collapsed point. Consider `relation_method = 'mantel'` + `mantel_kind = 'block_vs_col'` for a one-line-per-block visualisation.## `distance = -3` is negative; the env heatmaps will be pulled inward and may overlap the central point group. If a heatmap anchor becomes <= 0 you will get a warning and the corresponding heatmap may flip to the opposite side -- use a less negative value if that happens.## Warning: `distance = -3` is too negative for the current central layout -- at
## least one heatmap anchor became <= 0. The corresponding heatmap will flip to
## the opposite side or collapse onto the origin. Try a larger (less negative)
## `distance`.
p3[[1]]