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Box plot of tAge predictions with pairwise significance annotation

Source: R/plotting.R
tage_boxplot.Rd

Draws a box plot with jittered points for one prediction column, split by a grouping variable and optionally faceted by a subgroup. Pairwise comparisons are annotated with brackets; comparisons involving groups with too few observations, and — when p_threshold is set — non-significant ones, are dropped before plotting so the panel stays readable.

Usage

tage_boxplot(
  data,
  x_var,
  y_var,
  subgroup_var = NULL,
  colors = NULL,
  point_size = 2,
  point_alpha = 0.7,
  box_width = 0.5,
  stat_method = "t.test",
  comparisons = NULL,
  p_label = "p.signif",
  p_threshold = NULL,
  min_group_n = 2,
  font_size = 12,
  theme_type = "classic",
  title = NULL,
  xlab = NULL,
  ylab = NULL,
  legend_position = "right",
  y_center = NULL,
  y_min = NULL,
  y_max = NULL,
  facet_scales = "free_y",
  x_order = NULL,
  width = 10,
  height = 6
)

Arguments

data

Data frame of per-sample values, typically the prediction table returned by predict_tAge.

x_var

Column name defining the groups on the x axis.

y_var

Column name holding the values to plot, e.g. a *_tAge column.

subgroup_var

Optional column name used to facet the plot. Default NULL.

colors

Optional named vector of fill colours, keyed by the levels of x_var.

point_size, point_alpha

Size and opacity of the jittered points.

box_width

Width of the boxes.

stat_method

Test used for the pairwise comparisons, passed to ggpubr::stat_compare_means. Default "t.test".

comparisons

List of length-2 character vectors giving the pairs to test. Default NULL tests all pairs of x_var levels.

p_label

Label style for the annotations, e.g. "p.signif" for stars or "p.format" for numeric p-values.

p_threshold

If supplied, comparisons whose p-value is not below this threshold are removed from the plot. When faceting, a comparison is kept if it is significant in at least one facet.

min_group_n

Minimum number of non-missing observations required in both groups for a comparison to be shown. When faceting, every facet must meet it.

font_size

Base font size; also scales the annotation text.

theme_type

ggplot2 theme to apply, e.g. "classic" or "minimal".

title, xlab, ylab

Plot title and axis labels.

legend_position

Legend placement passed to ggplot2::theme.

y_center

If given, the y axis is made symmetric around this value — useful for relative predictions centred on zero.

y_min, y_max

Explicit y-axis limits, overriding the automatic range.

facet_scales

Scale behaviour across facets, passed to ggplot2::facet_wrap. Default "free_y".

x_order

Character vector giving the order of the x_var levels.

width, height

Plot size in inches, used to set the inline display size.

Value

A ggplot object.

See also

predict_tAge for producing the input table.

Examples

if (FALSE) { # \dontrun{
results <- predict_tAge(tAge_eset, model_paths, species = "mouse", mode = "EN")
tage_boxplot(
  results,
  x_var = "Genotype",
  y_var = "yugene_diff_EN_tAge",
  subgroup_var = "Tissue",
  x_order = c("WT", "Klotho KO"),
  ylab = "Relative tAge, months"
)
} # }