plot_specs_stacks: plot_specs_stacks

In darcyj/specificity: Calculate Environmental or Host Phylogenetic Specificity

plot_specs_stacks

Description

Visualizes results from phy_or_env_spec as stacked histograms. Aliased to plot_specificities() for backward compatibility.

Usage

plot_specs_stacks(
  specs_list,
  n_bins = 20,
  col_sig = "black",
  col_nsig = "gray",
  col_bord = NA,
  alpha = 0.05,
  label_cex = 1
)

Arguments

specs_list	list of data.frames. Each data.frame must be an output from phy_or_env_spec; must have columns "Spec" and "Pval".
n_bins	integer. Number of bins for stacked violins (default: 20).
col_sig	string. Color name or hex code for species where Pval <= alpha (default: "black").
col_nsig	string. Color name or hex code for species where Pval > alpha (default: "gray").
col_bord	string. Color name or hex code for border color. Use NA for no border (default: NA).
alpha	float. alpha value for determining statistical significance; see col_sig and col_nsig above (default: 0.05).
label_cex	float. Used to change size of x-axis labels (default: 1).

Value

returns nothing (a plot is made).

Author(s)

John L. Darcy

Examples

# library(specificity)
# attach(endophyte)
# # only analyze species with occupancy >= 20
# m <- occ_threshold(prop_abund(otutable), 20)
# # create list to hold phy_or_env_spec outputs
# specs_list <- list()
# specs_list$NDVI <- phy_or_env_spec(m, env=metadata$NDVI, 
#   n_cores=10, n_sim=50, p_method="gamma_fit")
# specs_list$Evapotranspiration <- phy_or_env_spec(m,
#   env=metadata$Evapotranspiration, n_cores=10, 
#   n_sim=100, p_method="gamma_fit")
# specs_list$Rainfall <- phy_or_env_spec(m, env=metadata$Rainfall,
#   n_cores=10, n_sim=50, p_method="gamma_fit")
# plot_specs_stacks(specs_list)

darcyj/specificity documentation built on Aug. 1, 2023, 8 a.m.