Skip to contents

Static scatterplot of percent1 vs percent2 from compute_pop()

Source: R/pop_plots.R
scatter_static.Rd

A ggplot2 scatterplot comparing prevalence in group a vs group b. Default coloring uses BH-corrected p-values computed per-plot from p_raw: "significant (BH)", "nominal only", "not significant". If only one category is present the plot falls back to p-value bins.

When color_by is supplied as a named vector, peptide metadata is joined and points matching the specified values are highlighted. Multiple groups may be given simultaneously:


  color_by = c("is_flagellum" = TRUE)
  color_by = c("species" = "Staphylococcus aureus")
  color_by = c("is_flagellum" = TRUE, "species" = "Staphylococcus aureus")

Usage

scatter_static(
  df,
  pair = NULL,
  rank = NULL,
  xlab = NULL,
  ylab = NULL,
  alpha = 0.05,
  color_by = NULL,
  color_title = NULL,
  ...
)

Arguments

df

A data frame with prevalence results.

pair

optional group pair (character length-2).

rank

optional single rank (character) to keep.

xlab, ylab

axis labels; defaults to pair[1]/pair[2] when pair is given.

alpha

numeric in (0,1]; significance threshold for category labels.

color_by

optional named vector identifying peptide-library values to highlight, e.g. c("is_flagellum" = TRUE) or c("species" = "Staphylococcus aureus").

color_title

optional legend title when color_by is used.

...

graphical parameters: point_size (default 2), point_alpha (default 0.85), jitter_width_pp (default 0), jitter_height_pp (default 0), font_family, font_size (default 12).

Value

A ggplot object.

Examples

set.seed(1)
prev <- data.frame(
  rank       = "peptide_id",
  feature    = paste0("pep", 1:30),
  group1     = "A",
  group2     = "B",
  prop1      = runif(30),
  prop2      = runif(30),
  percent1   = runif(30, 0, 100),
  percent2   = runif(30, 0, 100),
  ratio      = runif(30, 0.1, 10),
  p_raw      = runif(30),
  n_peptides = 1L
)

# basic plot
scatter_static(prev)


# filter to a specific pair and set axis labels
scatter_static(prev,
  pair  = c("A", "B"),
  xlab  = "Group A (%)",
  ylab  = "Group B (%)",
  alpha = 0.05
)