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Annotated Protein Diagram Configuration

Source: R/config_a3.R
A3Config.Rd

A serializable description of an A3 protein diagram. Build one with setup_A3Config() rather than calling this constructor directly.

Usage

A3Config(
  dat_path = NULL,
  title = NULL,
  origin = NULL,
  writer = NULL,
  n_per_row = 21L,
  position_every = 10L,
  ptm_placement = "radial",
  zoom = TRUE,
  residue_spacing = 0.3,
  marker_size = 28,
  font_size = 18,
  line_width = 2,
  show_markers = TRUE,
  show_labels = TRUE,
  region_opacity = 0.3,
  residue_fill = NULL,
  residue_stroke = NULL,
  label_color = NULL,
  pos_label_color = NULL,
  variant_color = NULL,
  disease_variant_color = NULL
)

Arguments

dat_path

Optional Character: Path to the data, read at draw time. The serializable alternative to passing data to draw().

title

Optional Character: Chart title. Declared here because it is the one property every chart type has; palette is not (four take a colormap instead), and axis labels and margins are cartesian-only.

origin

Optional Named character {"user", "default", "derived"}: Where each value came from, one entry per settable property. Absent on an authored config; written by the interface that resolved it.

writer

Optional Named character: Which interface wrote the config, as name and version. Absent on an authored config.

n_per_row

Integer [1, Inf): Residues per row.

position_every

Integer [1, Inf): Label every nth position.

ptm_placement

Character: How post-translational modifications are placed relative to the backbone.

zoom

Logical: Enable the zoom control.

residue_spacing

Numeric [0, Inf): Gap between residues.

marker_size

Numeric [0, Inf): Preferred residue marker size; reduced with related marks when needed to fit the surface.

font_size

Numeric [0, Inf): Residue label font size.

line_width

Numeric [0, Inf): Backbone line width.

show_markers, show_labels

Logical: Whether to draw each.

region_opacity

Numeric [0, 1]: Region band opacity.

residue_fill, residue_stroke

Optional Character: Residue marker colors.

label_color, pos_label_color

Optional Character: Label colors.

variant_color, disease_variant_color

Optional Character: Variant marker colors. NULL selects the corresponding light/dark A3 theme color.

Value

A3Config object.

Details

The bound data is an A3 object, created with rtemis.a3::create_A3().

Author

EDG

Examples

setup_A3Config(n_per_row = 30L)@type
#> [1] "a3"