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Publication-oriented admixture plots

plot_admix.Rd

`plot_admix()` is ggpop's native ggplot wrapper and always returns a ggplot object. It accepts full multi-K `ggpop_admix` data from `import_admix()` and filters with `k`; `k = "all"` renders joined K panels in the supported pophelper `plotQ(imgoutput = "join")` style. With `pop_group`, it supports individual labels, sorted individuals, group labels, and group-aware sorting. `plot_admixture_pophelper()` converts ggpop long-form admixture data to a pophelper qlist and calls `pophelper::plotQ()` for direct original-package compatibility; its return structure follows pophelper.

Usage

plot_admix(data, title = NULL, subtitle = NULL, caption = NULL,
  sort = c("none", "cluster", "all", "label"), sortind = NULL,
  k = "all", palette = NULL, group = "pop", order_group = FALSE,
  show_group_labels = NULL, subset_group = NULL, show_legend = FALSE,
  show_sample_labels = FALSE, base_size = 5, base_family = "",
  legend_position = "top", pop_group = TRUE, bar_width = 1, ...)
as_pophelper_qlist(data)
plot_admixture_pophelper(data, ..., exportplot = FALSE, returnplot = TRUE,
  theme = "theme_bw", basesize = 8)

Arguments

data

A `ggpop_admix` object.

title, subtitle, caption

Plot text.

sort, sortind

Native and pophelper-compatible sample ordering modes.

k

K selection: `"all"`, a single integer, or an integer vector such as `c(2, 4)`.

palette

Named or unnamed cluster colours.

group, order_group, show_group_labels, subset_group

Population group column and pophelper-style group controls.

show_legend, show_sample_labels

Legend and sample-label display switches.

base_size, base_family, legend_position

Admixture plot theme settings aligned with the supported pophelper `plotQ()` subset.

pop_group

Set to `FALSE` to disable population group facets.

bar_width

Admixture bar width.

...

Additional arguments passed to `geom_admix()` or `pophelper::plotQ()`.

exportplot, returnplot, theme, basesize

Arguments forwarded to `pophelper::plotQ()`.

Details

The pophelper-style user-facing admixture plotting interfaces are `plot_admix()` and `geom_admix()`. Use `plot_admix2()` or `geom_admix2()` when you want the cleaner pure ggplot facet layout. `plot_admixture_pophelper()` is an advanced compatibility escape hatch for users who need original pophelper behavior.