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Plot enrichment counts per group (and optional interaction)

Source: R/alpha_plots.R
plot_enrichment_counts.Rd

Visualizes per-sample peptide enrichment counts across groups in a <phip_data> object, with optional interaction of multiple grouping variables. Presence is defined by exist > 0. The plot(s) are produced by an internal helper .plot_enrichment_counts_one().

Usage

plot_enrichment_counts(
  phip_data,
  group_cols = NULL,
  prevalence_threshold = 0.05,
  custom_colors = NULL,
  binwidth = 1,
  group_interaction = FALSE,
  interaction_only = FALSE,
  interaction_sep = " * ",
  annotation_size = 4,
  ...
)

Arguments

phip_data

A <phip_data> object with data_long containing at least sample_id, peptide_id, and exist.

group_cols

Character vector of grouping columns in data_long, or NULL to plot all samples together.

prevalence_threshold

Numeric in [0,1]; minimum prevalence used by .plot_enrichment_counts_one() to filter/annotate bins (default 0.05).

custom_colors

Optional named vector for group colors passed through to .plot_enrichment_counts_one() (default NULL).

binwidth

Numeric bin width for histograms (default 1).

group_interaction

Logical; also compute a plot for the interaction of all group_cols (default FALSE).

interaction_only

Logical; if TRUE, return only the interaction plot (requires group_interaction = TRUE and at least two group_cols).

interaction_sep

Character separator for interaction labels (default " * ").

annotation_size

Numeric; size of the in-plot threshold annotations (passed to geom_text(size = ...)). Typical range 3–6. Default 4.

...

Reserved for future extensions; ignored.

Value

  • A single plot object (when group_cols = NULL, or when only one plot is produced), or

  • A named list of plot objects (when multiple plots are produced).

Details

  • If group_cols = NULL, a single plot is returned for all samples.

  • If group_cols is a character vector, a list of plots is returned (one per grouping column) unless interaction_only = TRUE.

  • If group_interaction = TRUE and at least two group_cols are supplied, an additional interaction plot is created whose label joins groups using interaction_sep.

  • If interaction_only = TRUE, only the interaction plot is returned (this requires group_interaction = TRUE and at least two group_cols).

Examples

# per-group plots
pd <- load_example_data()
p <- plot_enrichment_counts(pd, group_cols = c("group","timepoint"))
#> [18:40:45] INFO  Plotting enrichment counts (<phip_data>)
#>                  -> group_cols: 'group', 'timepoint'
#> [18:40:45] INFO  building enrichment count plot
#>                  -> grouping variable: 'group'
#> [18:40:45] OK    plot built
#> [18:40:45] OK    building enrichment count plot - done
#>                  -> elapsed: 0.266s
#> [18:40:45] INFO  building enrichment count plot
#>                  -> grouping variable: 'timepoint'
#> [18:40:45] OK    plot built
#> [18:40:45] OK    building enrichment count plot - done
#>                  -> elapsed: 0.54s
#> [18:40:45] OK    Plotting enrichment counts (<phip_data>) - done
#>                  -> elapsed: 0.808s

# add interaction plot
p2 <- plot_enrichment_counts(pd,
  group_cols = c("group","timepoint"),
  group_interaction = TRUE
)
#> [18:40:45] INFO  Plotting enrichment counts (<phip_data>)
#>                  -> group_cols: 'group', 'timepoint'
#> [18:40:45] INFO  building enrichment count plot
#>                  -> grouping variable: 'group'
#> [18:40:46] OK    plot built
#> [18:40:46] OK    building enrichment count plot - done
#>                  -> elapsed: 0.228s
#> [18:40:46] INFO  building enrichment count plot
#>                  -> grouping variable: 'timepoint'
#> [18:40:46] OK    plot built
#> [18:40:46] OK    building enrichment count plot - done
#>                  -> elapsed: 0.232s
#> [18:40:46] INFO  building enrichment count plot
#>                  -> grouping variable: '..phip_interaction..'
#> [18:40:46] OK    plot built
#> [18:40:46] OK    building enrichment count plot - done
#>                  -> elapsed: 0.227s
#> [18:40:46] OK    Plotting enrichment counts (<phip_data>) - done
#>                  -> elapsed: 0.696s

# interaction only
p3 <- plot_enrichment_counts(pd,
  group_cols = c("group","timepoint"),
  group_interaction = TRUE,
  interaction_only = TRUE
)
#> [18:40:46] INFO  Plotting enrichment counts (<phip_data>)
#>                  -> group_cols: 'group', 'timepoint'
#> [18:40:46] INFO  building enrichment count plot
#>                  -> grouping variable: '..phip_interaction..'
#> [18:40:46] OK    plot built
#> [18:40:46] OK    building enrichment count plot - done
#>                  -> elapsed: 0.24s
#> [18:40:46] OK    Plotting enrichment counts (<phip_data>) - done
#>                  -> elapsed: 0.248s