geneviewer (version 0.1.10)

GC_sequence: Update Sequence Display of a GC Chart Cluster

Description

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

Usage

GC_sequence(
  GC_chart,
  show = TRUE,
  cluster = NULL,
  y = 50,
  sequenceStyle = list(),
  markerStyle = list(),
  ...
)

Value

An updated GC chart with modified sequence display settings.

Arguments

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 50).

sequenceStyle

A list of styling options for the sequence line.

markerStyle

A list of styling options for the sequence break markers.

...

Additional customization arguments for sequence display.

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)