plot_specs_violin: plot_specs_violin

In darcyj/specificity: Calculate Environmental or Host Phylogenetic Specificity

plot_specs_violin

Description

Visualizes results from phy_or_env_spec as violins. Violin area is proportionally divided such that lighter colors represent density of non-significant features, and darker colors represent statistically significant features.

Usage

plot_specs_violin(
  specs_list,
  cols = "black",
  cols_bord = "white",
  alpha = 0.05,
  label_cex = 1,
  nsig_trans = 0.3,
  minval = -1,
  maxval = 1,
  ylab = "Spec",
  ...
)

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".
cols	character vector of color names or hex codes. If only one value is given, all violins will be that color. Otherwise, one value may be given per item in specs_list, corresponding to its order (default: "black").
cols_bord	character vector of color names or hex codes. Color name or hex code for borders drawn around and within violins. Length 1 or length n, just like cols. For no borders, use cols_bord=NA (default: "white").
alpha	float. alpha value for determining statistical significance (default: 0.05).
label_cex	float. Used to change size of x-axis labels (default: 1).
nsig_trans	float between 0 and 1 (inclusive). Determines how transparent violin area will be for nonsignificant features, with 0 meaning totally transparent and 1 meaning totally opaque (default: 0.4).
minval	minimum possible value for specificity statistic (default: -1).
maxval	maximum possible value for specificity statistic (default: 1).
ylab	y-axis label for plot (default:"Spec").
...	additional arguments to be passed to polygon().

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", 
#   denom_type="sim_center")
# specs_list$Evapotranspiration <- phy_or_env_spec(m,
#   env=metadata$Evapotranspiration, n_cores=10, 
#   n_sim=100, p_method="gamma_fit",
#   denom_type="sim_center")
# specs_list$Rainfall <- phy_or_env_spec(m, env=metadata$Rainfall,
#   n_cores=10, n_sim=50, p_method="gamma_fit", 
#   denom_type="sim_center")
# # default black
# plot_specs_violin(specs_list)
# # with colors
# plot_specs_violin(specs_list, cols=c("forestgreen", "gold", "blue"))
# # with border colors
# plot_specs_violin(specs_list, cols=c("forestgreen", "gold", "blue"),
#   cols_bord=c("red", "blue", "black"))
# # with thicker borders (arg "lwd" is passed to polygon())
# plot_specs_violin(specs_list, cols=c("forestgreen", "gold", "blue"),
#   cols_bord="black", lwd=3)
# # with NO borders
# plot_specs_violin(specs_list, cols=c("forestgreen", "gold", "blue"),
#   cols_bord=NA)

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