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Delta-prevalence vs Pooled Prevalence

Source: R/delta_plots.R
deltaplot.Rd

Build a static ggplot showing the per-peptide shift in prevalence (\(\Delta = group2 - group1\)) as a function of pooled prevalence (\((group1 + group2)/2\)). The input should be a tibble/data frame produced by ph_compute_prevalence() or equivalent with columns group1, group2, prop1, and prop2.

Usage

deltaplot(
  prev_tbl,
  group_pair_values = NULL,
  group_labels = NULL,
  point_jitter_width = 0.005,
  point_jitter_height = 0.005,
  point_alpha = 0.25,
  point_size = 0.6,
  add_smooth = TRUE,
  smooth_k = 5,
  arrow_color = "red",
  arrow_head_length_mm = 4,
  arrow_x_frac = 0.97,
  plot_title = NULL,
  plot_subtitle = NULL,
  x_label = NULL,
  y_label = NULL
)

Arguments

prev_tbl

Data frame with columns group1, group2, prop1, prop2. Optional feature is used for row identity only.

group_pair_values

Optional length-2 character vector c(group1, group2). Use this when prev_tbl contains multiple group pairs.

group_labels

Optional length-2 character vector of display labels c(label_group1, label_group2). Defaults to group1/group2.

point_jitter_width, point_jitter_height

Jitter amounts for the points. Defaults 0.005.

point_alpha

Point transparency. Default 0.25.

point_size

Point size. Default 0.6.

add_smooth

Add a GAM smooth curve (mgcv). Default TRUE.

smooth_k

Basis dimension k for the smooth. Default 5.

arrow_color

Color for the directional arrows and labels. Default "red".

arrow_head_length_mm

Arrow head length in mm. Default 4.

arrow_x_frac

Arrow X position as a fraction of the max pooled prevalence. Default 0.97 (near the right edge).

plot_title, plot_subtitle

Optional plot labels for the title/subtitle.

x_label, y_label

Optional axis labels. Defaults are generated from the group labels.

Value

A ggplot object.

Details

The plot places each feature (peptide) as a point at:

  • x-axis: pooled prevalence (prop1 + prop2)/2

  • y-axis: prevalence shift (prop2 - prop1)

Points are optionally jittered for visibility. A dashed horizontal line marks \(\Delta = 0\). Optional arrows and labels indicate the direction of increased prevalence for group1 vs group2. If add_smooth = TRUE, a GAM smooth is overlaid to summarize the trend across pooled prevalence.

Examples

set.seed(1)
n <- 40
prev_tbl <- data.frame(
  feature = paste0("pep", seq_len(n)),
  group1  = "A",
  group2  = "B",
  prop1   = runif(n),
  prop2   = runif(n)
)

p <- deltaplot(
  prev_tbl,
  group_pair_values = c("A", "B"),
  group_labels      = c("Group A", "Group B")
)
#> [18:40:37] INFO  Preparing delta prevalence plot.
print(p)