Visualize multi-orientation environmental–species correlation heatmaps

Usage

gglink_heatmaps(
  env,
  spec,
  env_select = NULL,
  spec_select = NULL,
  spec_layout = "circle_outline",
  spec_orientation = c("up", "down", "left", "right"),
  spec_relation = TRUE,
  relation_method = c("correlation", "mantel"),
  cor.method = c("pearson", "kendall", "spearman"),
  cor.use = c("everything", "all", "complete", "pairwise", "na"),
  mantel.method = c("mantel", "mantel.partial", "mantelhaen.test", "mantel.correlog"),
  mantel.method2 = c("pearson", "kendall", "spearman"),
  mantel.alternative = c("two.sided", "less", "greater"),
  drop_nonsig = FALSE,
  shape = 22,
  distance = 3,
  fontsize = 5,
  orientation = c("top_right", "bottom_right", "top_left", "bottom_left"),
  r = 6
)

Arguments

env: Data Frame A data frame or matrix containing environmental variables. Each column represents an environmental factor.
spec: Data Frame A data frame or matrix containing species abundance or trait data. Each column represents a species or taxonomic unit.
env_select: Optional list specifying the column indices (or names) of environmental variables to include in each environmental block. Each list element corresponds to one quadrant of the heatmap layout.
spec_select: Optional list specifying column indices (or names) of species to include. If multiple elements are provided, they define separate species clusters in the visualization.
spec_layout: Character Character string specifying the spatial arrangement of species nodes. Options include `"ringle"` (radial) and other supported layouts.
spec_orientation: Character spec_oritation. Options include: "up","down","left","right"
spec_relation: Logical (defalt = TRUE) Whether to compulate the ralationship of spec
relation_method: Character Method for computing relationships between species and environmental factors. Options are `"correlation"` or `"mantel"`.
cor.method: Character Correlation method to use when `relation_method = "correlation"`. One of `"pearson"`, `"kendall"`, or `"spearman"`.
cor.use: Character Method for handling missing values in correlation computation. One of `"everything"`, `"all"`, `"complete"`, `"pairwise"`, or `"na"`.
mantel.method: Character Type of Mantel test to use when `relation_method = "mantel"`. Options include `"mantel"`, `"mantel.partial"`, `"mantelhaen.test"`, and `"mantel.correlog"`.
mantel.method2: Character Correlation coefficient used in the Mantel test. One of `"pearson"`, `"kendall"`, or `"spearman"`.
mantel.alternative: Character Alternative hypothesis for Mantel test. One of `"two.sided"`, `"less"`, or `"greater"`.
drop_nonsig: Logical if `TRUE`, non-significant correlations are dropped from the final visualization.
shape: Intrger Integer or numeric specifying the shape of species nodes in the plot (passed to `geom_point()`).
distance: Numeric the offset distance between central nodes and the environmental heatmaps.
fontsize: Numeric (default = 5) The fontsize in env heatmap
orientation: Character Character vector defining which heatmap quadrants to display. Can include any combination of `"top_right"`, `"bottom_right"`, `"top_left"`, and `"bottom_left"`.
r: Numeric radius of the central species layout (in plot units).

Value

a list of ggplot2

Examples

NULL
#> NULL