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Interactive Delta-prevalence vs Pooled Prevalence

Source: R/delta_plots.R
deltaplot_interactive.Rd

Build an interactive plotly chart 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_interactive(
  prev_tbl,
  group_pair_values = NULL,
  group_labels = NULL,
  point_alpha = 0.6,
  point_size = 6,
  add_smooth = TRUE,
  smooth_k = 5,
  arrow_color = "red",
  arrow_x_frac = 0.97,
  arrow_length_frac = 0.3,
  label_x_gap_frac = 0.03,
  label_y_gap_frac = 0.02,
  plot_title = NULL,
  plot_subtitle = NULL,
  point_jitter_width = 0.005,
  point_jitter_height = 0.005
)

Arguments

prev_tbl

Data frame with columns group1, group2, prop1, prop2. Optional feature is used for labels.

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_alpha

Point transparency. Default 0.6.

point_size

Point size. Default 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_x_frac

Arrow X position as a fraction of the x-range. Default 0.97.

arrow_length_frac

Arrow length as a fraction of the y-range. Default 0.30.

label_x_gap_frac

Horizontal label offset as a fraction of the x-range.

label_y_gap_frac

Vertical label offset as a fraction of the y-range.

plot_title, plot_subtitle

Optional plot labels for the title/subtitle.

point_jitter_width, point_jitter_height

Jitter amounts. Defaults 0.005.

Value

A plotly 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 display, and hover text includes the feature identifier plus prevalence (percent and proportion) and counts (n1, N1, n2, N2) when available in the input table. 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.

Examples

if (FALSE) { # \dontrun{
set.seed(2)
n <- 40
prev_tbl <- data.frame(
  feature = paste0("pep", seq_len(n)),
  group1  = "A",
  group2  = "B",
  prop1   = runif(n),
  prop2   = runif(n)
)

p <- deltaplot_interactive(
  prev_tbl,
  group_pair_values = c("A", "B"),
  group_labels      = c("Group A", "Group B"),
  add_smooth        = FALSE
)
p
} # }