scatter_dist: Plot scatterplots of genetic distance vs landscape distance

In graph4lg: Build Graphs for Landscape Genetics Analysis

Plot scatterplots of genetic distance vs landscape distance

Description

The function enables to plot scatterplots to visualize the relationship between genetic distance (or differentiation) and landscape distance (Euclidean distance, cost-distance, etc.)between populations or sample sites.

Usage

scatter_dist(
  mat_gd,
  mat_ld,
  method = "loess",
  thr_gd = NULL,
  thr_ld = NULL,
  se = TRUE,
  smooth_col = "black",
  pts_col = "#999999"
)

Arguments

mat_gd	A symmetric matrix or dist object with pairwise genetic distances between populations or sample sites.
mat_ld	A symmetric matrix or dist object with pairwise landscape distances between populations or sample sites. These distances can be Euclidean distances, cost-distances or resistance distances, among others.
method	A character string indicating the smoothing method used to fit a line on the scatterplot. Possible values are the same as with function 'geom_smooth()' from ggplot2 : 'lm', 'glm', 'gam', 'loess' (default).
thr_gd	(optional) A numeric or integer value used to remove values from the data before to plot. All genetic distances values above thr_gd are removed from the data.
thr_ld	(optional) A numeric or integer value used to remove values from the data before to plot. All landscape distances values above thr_ld are removed from the data.
se	Logical (optional, default = TRUE) indicating whether the confidence interval around the smooth line is displayed.
smooth_col	(optional) A character string indicating the color used to plot the smoothing line (default: "blue"). It must be a hexadecimal color code or a color used by default in R.
pts_col	(optional) Character string indicating the color used to plot the points (default: "#999999"). It must be a hexadecimal color code or a color used by default in R.

Details

IDs in mat_gd and mat_ld must be the same and refer to the same sampling sites or populations, and both matrices must be ordered in the same way. Matrix of genetic distance mat_gd can be computed using mat_gen_dist. Matrix of landscape distance mat_ld can be computed using mat_geo_dist when the landscape distance needed is a Euclidean geographical distance.

Value

A ggplot2 object to plot

Author(s)

P. Savary

Examples

data(data_tuto)
mat_dps <- data_tuto[[1]]
mat_dist <- suppressWarnings(mat_geo_dist(data = pts_pop_simul,
      ID = "ID",
      x = "x",
      y = "y"))
mat_dist <- mat_dist[order(as.character(row.names(mat_dist))),
                      order(as.character(colnames(mat_dist)))]
scatterplot_ex <- scatter_dist(mat_gd = mat_dps,
                              mat_ld = mat_dist)

graph4lg documentation built on Feb. 16, 2023, 5:43 p.m.