Plot alpha diversity (precomputed) — interactive (plotly)

native plotly version of plot_alpha(). mirrors the ggplot look: per-group boxplots with jittered points and optional faceting by rank.

Usage

plot_alpha_interactive(
  x,
  metric = c("richness", "shannon_diversity", "simpson_diversity", "pielou_evenness",
    "berger_parker_dominance"),
  group_col = "group",
  rank_col = "rank",
  filter_groups = NULL,
  filter_ranks = NULL,
  custom_colors = NULL,
  facet_by_rank = TRUE,
  ncol = 2,
  facet_scales = "fixed",
  interaction_only = FALSE,
  interaction_sep = NULL,
  x_order = NULL,
  x_labels = NULL,
  y_range = NULL,
  x_tickangle = 0,
  quartile_method = c("exclusive", "inclusive", "linear"),
  jitter_width = 0.25,
  point_size = 6,
  point_alpha = 0.85,
  text_size = 12,
  font_family = "Montserrat",
  show_grids = TRUE,
  ...
)

Arguments

x: a "phip_alpha_diversity" list (output of compute_alpha()) or a single alpha-diversity data frame.
metric: one of "richness", "shannon_diversity", "simpson_diversity", "pielou_evenness", or "berger_parker_dominance".
group_col: name of the grouping column in the alpha table (default "group" when group_cols = NULL in the computation step).
rank_col: name of the rank column (default "rank").
filter_groups: optional character vector; keep only these group levels.
filter_ranks: optional character vector; keep only these ranks.
custom_colors: named character vector of hex colors for groups (like ggplot scale_fill_manual()).
facet_by_rank: logical; facet by rank_col if multiple ranks present.
ncol: integer; number of columns in facet wrap (default 2).
facet_scales: "fixed", "free_x", "free_y", or "free".
interaction_only: logical; if TRUE, plot only the interaction table (when available in x). useful when compute_alpha() was run with group_interaction = TRUE.
interaction_sep: character; separator used to join interaction labels. default is taken from attr(x, "interaction_sep") if present, otherwise " * ".
x_order: optional character vector with desired group order (levels).
x_labels: optional named character vector mapping group -> label (used on x axis).
y_range: optional numeric length-2; y axis range (e.g., c(0, 2300)).
x_tickangle: numeric; tick label rotation in degrees (default 0; e.g., 25).
quartile_method: one of c("exclusive","inclusive","linear"); passed to plotly box (default "exclusive" ~ ggplot).
jitter_width: Numeric; horizontal jitter width for points.
point_size: Numeric; size of jittered points.
point_alpha: Numeric in (0,1); alpha for jittered points.
text_size: Numeric; base text size for plot labels.
font_family: Character; font family for plot text.
show_grids: Logical; whether to show panel grid lines.
...: Reserved for future extensions; ignored.

Value

A plotly htmlwidget.

Examples

if (FALSE) { # \dontrun{
plot_alpha_interactive(df, metric = "richness", group_col = "group")
} # }