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Draw generic genomic features

Source: R/geom-feature.R
geom_feature.Rd

A general layer for CDS, tRNA, rRNA, repeat, CRISPR, promoter or user-defined features. It supports directional arrows, blocks, notched chevrons and lollipops, all generated against the sequence's real local curve. Feature fill and geometry use independent role-specific scales.

Usage

geom_feature(
  mapping = NULL,
  data = NULL,
  type = "type",
  category = NULL,
  label = "label",
  feature_shape = "arrow",
  feature_colors = NULL,
  feature_width = NULL,
  feature_offset = NULL,
  feature_order = NULL,
  show_legend = TRUE,
  legend_position = "right",
  ...
)

Arguments

mapping

Optional aesthetic mapping. Role aesthetics such as seq_id, start, end and strand may rename input columns; ordinary visual mappings are evaluated after geometry is generated.

data

data.frame with seq_id, start, end and strand; optional type, category and label.

type

Column name used as the feature type, default "type".

category

Optional column name used for colour grouping; defaults to type.

label

Optional column name used for annotation text; defaults to label when present, otherwise type.

feature_shape

Fixed feature geometry used when feature_shape is not mapped in aes(): "arrow", "block", "chevron", or "lollipop". The default is "arrow". Use aes(feature_shape = type) together with scale_feature_shape_manual() to map categories to geometry.

feature_colors

Optional named color vector by feature value; unnamed vectors are recycled positionally.

feature_width

Optional numeric or named vector controlling feature width; passed to geom_gene(gene_width = ...).

feature_offset

Optional numeric or named vector controlling feature offset; passed to geom_gene(gene_offset = ...).

feature_order

Optional feature order for the legend.

show_legend

Logical. Show the feature legend, default TRUE.

legend_position

Position of the feature legend: "left", "right", "top", "bottom" or "inside".

...

Additional arguments passed to geom_gene().

Value

A list of ggplot2 layers

Examples

library(ggchord)
data(seq_data_example)
features <- data.frame(seq_id = "MT108731.1",
                       start = 1000, end = 4000,
                       strand = "+", type = "CDS")
p <- ggchord(seq_data_example) + geom_seq() + geom_feature(features)
p