One function for all alpha diversity visualizations.
Usage
plot_alpha(
data.obj,
plot.type = c("boxplot", "spaghettiplot", "dotplot"),
alpha.name = c("shannon", "observed_species"),
alpha.obj = NULL,
depth = NULL,
subject.var = NULL,
time.var = NULL,
group.var = NULL,
strata.var = NULL,
time.points = NULL,
change.type = c("none", "relative", "log_fold", "absolute"),
theme = "bw",
...
)Arguments
- data.obj
A MicrobiomeStat data object containing feature.tab, meta.dat, and optionally feature.ann, tree, and feature.agg.list.
- plot.type
Type of visualization: - "boxplot": Box plots comparing groups/time points - "spaghettiplot": Individual trajectories (longitudinal) - "dotplot": Dot plot of per-time statistics (longitudinal)
- alpha.name
Character vector. Alpha diversity indices to calculate. Options: "shannon", "simpson", "observed_species", "chao1", "ace", "pielou".
- alpha.obj
Optional pre-calculated alpha diversity object.
- depth
Rarefaction depth. NULL for no rarefaction.
- subject.var
Character. Name of the subject/sample ID variable in meta.dat. Required for longitudinal and paired designs.
- time.var
Character. Name of the time variable in meta.dat. NULL for cross-sectional studies.
- group.var
Character. Name of the grouping variable (e.g., treatment, condition).
- strata.var
Character. Name of the stratification variable for faceting.
- time.points
Time point specification. Can be: - NULL: use all available time points (auto-detect design) - Single value: cross-sectional at that time point - Vector of 2: paired design (baseline, followup) - Vector of >2: longitudinal with specific time points - List: list(baseline = "T0", followup = c("T1", "T2"))
- change.type
For paired/longitudinal comparisons: - "none": show raw values (default) - "relative": relative change (x1-x0)/(x1+x0) - "log_fold": log2 fold change - "absolute": absolute difference
- theme
Theme specification. Can be: - Character: preset name ("bw", "classic", "minimal", "prism") - List: list(base.size = 12, choice = "bw", palette = NULL)
- ...
Additional arguments passed to the underlying function.
Examples
if (FALSE) { # \dontrun{
data(peerj32.obj)
# Cross-sectional alpha boxplot
plot_alpha(peerj32.obj, "boxplot",
alpha.name = c("shannon", "observed_species"),
group.var = "group")
# Longitudinal spaghettiplot
plot_alpha(peerj32.obj, "spaghettiplot",
subject.var = "subject",
time.var = "time",
alpha.name = "shannon",
group.var = "group")
} # }