Add an alignment ribbon layer — geom

Draws colored ribbons corresponding to alignment results. Color scheme and spacing parameters are specified here.

Usage

geom_ribbon(
  mapping = NULL,
  data = NULL,
  ribbon_color_scheme = NULL,
  ribbon_colors = NULL,
  ribbon_color_by = NULL,
  ribbon_color_limits = NULL,
  ribbon_color_breaks = NULL,
  ribbon_color_name = NULL,
  ribbon_alpha = NULL,
  ribbon_alpha_by = NULL,
  ribbon_alpha_range = c(0.15, 0.9),
  ribbon_ctrl_point = NULL,
  ribbon_gap = NULL,
  alpha = NULL,
  ribbon_outline_color = "black",
  ribbon_outline_width = 0.05,
  ribbon_outline_linetype = 1,
  ribbon_outline_by = NULL,
  ribbon_outline_colors = NULL,
  ribbon_linetype_by = NULL,
  ribbon_linetypes = NULL,
  ribbon_direction = c("none", "alpha", "outline", "linetype"),
  ribbon_direction_colors = c(same = "black", reverse = "grey50"),
  ribbon_direction_linetypes = c(same = "solid", reverse = "dashed"),
  ribbon_direction_alpha = c(same = 1, reverse = 0.45),
  show_legend = TRUE,
  legend_position = "left",
  legend_key_width = NULL,
  legend_key_height = NULL,
  ...
)

Arguments

mapping: Default NULL (uses pre-computed data)
data: Default NULL (retrieved automatically from the layout)
ribbon_color_scheme: Character. Color scheme "pident", "query", "subject" or "single", default "pident"
ribbon_colors: Optional color vector. Ribbon color parameters
ribbon_color_by: Optional character column name. When set, ribbon fill is mapped to a continuous colourbar for that numeric column instead of pident (e.g. "bitscore").
ribbon_color_limits: Optional numeric length-2 limits for ribbon_color_by.
ribbon_color_breaks: Optional numeric breaks for the ribbon_color_by colourbar.
ribbon_color_name: Optional legend title for the ribbon_color_by colourbar (defaults to the column name).
ribbon_alpha: Numeric (0-1). Ribbon transparency, default 0.35
ribbon_alpha_by: Optional character column name. When set, alpha is scaled continuously from that numeric column.
ribbon_alpha_range: Numeric length-2. Alpha range used by ribbon_alpha_by, default c(0.15, 0.9).
ribbon_ctrl_point: Optional vector/list. Bezier control points, default c(0,0)
ribbon_gap: Optional numeric/vector. Spacing between sequences and ribbons, default 0.15
alpha: Ribbon transparency (overrides ribbon_alpha), defaults to the value used in the layout
ribbon_outline_color: Character. Color of the ribbon outline (border), default "black"
ribbon_outline_width: Numeric. Line width of the ribbon outline, default 0.05
ribbon_outline_linetype: Numeric or character. Line type of the ribbon outline, default 1 (solid); see linetype in ggplot2 for options
ribbon_outline_by: Optional discrete column name. When set, outline colour is mapped by that column and ribbon_outline_colors controls the palette.
ribbon_outline_colors: Optional named color vector for ribbon_outline_by; unnamed vectors are recycled positionally.
ribbon_linetype_by: Optional discrete column name. When set, outline linetype is mapped by that column and ribbon_linetypes controls the values.
ribbon_linetypes: Optional named linetype vector for ribbon_linetype_by.
ribbon_direction: Character. How to visually distinguish same- vs reverse-orientation alignments: "none", "alpha", "outline" or "linetype".
ribbon_direction_colors: Named color vector with same and reverse entries, used when ribbon_direction = "outline".
ribbon_direction_linetypes: Named linetype vector with same and reverse entries, used when ribbon_direction = "linetype".
ribbon_direction_alpha: Named numeric vector with same and reverse entries, used when ribbon_direction = "alpha".
show_legend: Whether to show the legend, default TRUE
legend_position: Position of this layer's legend (the Identity( colourbar): one of "left", "right", "top", "bottom" or "inside", default "left". Pass NULL to let the legend follow theme(legend.position = ...) together with the other legends.
legend_key_width: Optional width of the Identity( Accepts a grid unit, e.g. unit(1, "cm"), or a number interpreted as centimetres. Default NULL uses the ggplot2 default width.
legend_key_height: Optional height of the Identity( Accepts a grid unit, e.g. unit(5, "cm"), or a number interpreted as centimetres. Default NULL lets the vertical bar fill the available height (and uses a fixed height for horizontal legends).
...: Additional arguments passed to geom_polygon()

Value

A list of ggplot2 layers

Examples

library(ggchord)
data(seq_data_example)
data(ribbon_data_example)
p <- ggchord(seq_data_example, ribbon_data_example) +
  geom_seq() + geom_ribbon()
p