Interactive prevalence scatter for prevalence results

Creates an interactive scatter (plotly) comparing prevalence in group a vs group b for per-feature results produced by compute_pop(). Accepts a plain data.frame with columns percent1, percent2, feature, group1, group2, p_raw, etc.

When pair is given, subsetting uses .ph_filter_pairs().

Color mapping:

Default (color_by = NULL): BH-corrected p-values computed per-plot from p_raw ("significant (BH)", "nominal only", "not significant").

color_by as a named vector highlights points matching the specified peptide-library values:


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

Usage

scatter_interactive(
  df,
  pair = NULL,
  rank = NULL,
  xlab = NULL,
  ylab = NULL,
  alpha = 0.05,
  color_by = NULL,
  color_title = NULL,
  peplib = NULL,
  background_df = NULL,
  ...
)

Arguments

df: A data.frame with columns percent1, percent2, feature, group1, group2, p_raw, optionally n_peptides, rank, peptide_id.
pair: optional length-2 character, e.g. c("kid_serum::T2","kid_serum::T8").
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; not the plotly alpha.
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.
peplib: Optional peptide metadata table used to resolve color_by when not available via the global library.
background_df: Optional data frame of background points.
...: graphical parameters: category_colors, show_background, background_name, background_color, background_size, background_alpha, background_max_n, background_seed, point_line_width, point_line_color, point_size, point_alpha, jitter_width_pp, jitter_height_pp, font_family, font_size.

Value

a plotly object.

Examples

if (FALSE) { # \dontrun{
p <- scatter_interactive(scatters,
  pair        = c("kid_serum::T2", "kid_serum::T8"),
  rank        = "peptide_id",
  color_by    = c("is_flagellum" = TRUE),
  color_title = "Flagellum"
)
p
} # }