Update Sequence Display of a GC Chart Cluster

Modify the sequence display and break markers of specified clusters within a GC chart.

Usage

GC_sequence(
  GC_chart,
  show = TRUE,
  cluster = NULL,
  y = NULL,
  sequenceStyle = list(),
  markerStyle = list(),
  ...
)

Arguments

Argument	Description
GC_chart	A GC chart object.
show	Logical, whether to display the sequence (default is TRUE).
cluster	Numeric or character vector specifying clusters to update.
y	Vertical position of the sequence line. Default is NULL: as set by the theme, otherwise 50.
sequenceStyle	A list of styling options for the sequence line.
markerStyle	A list of styling options for the sequence break markers, e.g. markerHeight, tiltAmount and gap (distance in pixels between each marker and the break), plus any CSS style.
...	Additional customization arguments for sequence display.

Value

An updated GC chart with modified sequence display settings.

Details

This function allows customization of the sequence line and break markers in a GC chart. It offers options to adjust the sequence line (sequenceStyle) and break markers (markerStyle). The y parameter can be used to set the vertical position of the sequence.

Examples

genes_data <- data.frame(
  start = c(10, 90, 130, 170, 210),
  end = c(40, 120, 160, 200, 240),
  name = c('Gene 1', 'Gene 3', 'Gene 4', 'Gene 5', 'Gene 6'),
  group = c('A', 'B', 'B', 'A', 'C'),
  cluster = c(1, 1, 2, 2, 2)
)

# Basic usage
GC_chart(genes_data, cluster ="cluster", group = "group", height = "200px") %>%
GC_labels("name") %>%
GC_sequence(show = TRUE, y = 50, cluster = NULL)

# Customize sequence and marker styles
GC_chart(genes_data, cluster="cluster", group = "group", height = "200px") %>%
  GC_scale(hidden = TRUE, scale_breaks = TRUE) %>%
  GC_sequence(
    start = NULL,
    end = NULL,
    sequenceStyle = list(
      stroke = "blue",
      strokeWidth = 1
      # Any other CSS style
    ),
    markerStyle = list(
      stroke = "blue",
      strokeWidth = 1,
      gap = 3,
      tiltAmount = 5
      # Any other CSS style
    )
  ) %>%
  GC_legend(FALSE)