Create a GC Chart Visualization

Generates an interactive GC chart for genomic data.

Usage

GC_chart(
  data,
  start = "start",
  end = "end",
  cluster = NULL,
  group = NULL,
  strand = NULL,
  width = "100%",
  height = "400px",
  style = list(),
  elementId = NULL,
  save_button = TRUE
)

Arguments

Argument	Description
data	Data frame containing genomic information or the file path to a folder containing .gbk files. When providing a file path, the data is loaded and processed into a data frame internally.
start	Column name that indicates start positions. Default is "start".
end	Column name that indicates end positions. Default is "end".
cluster	Optional column name used for clustering purposes. Default is NULL.
group	Column name used for gene grouping to influence color aesthetics.
strand	Optional column name indicating strand orientation. Acceptable values include 1, 'forward', 'sense', or '+' to represent the forward strand, and -1, 0, 'reverse', 'antisense', "complement" or '-' to represent the reverse strand. Default is NULL, meaning strand information is not used.
width	Width specification for the chart, such as '100%' or 500. Default is unspecified.
height	Height specification for the chart, such as '400px' or 300. Default is unspecified.
style	A list of CSS styles to be applied to the chart container. Each element of the list should be a valid CSS property-value pair. For example, list(backgroundColor = "white", border = "2px solid black"). Default is an empty list.
elementId	Optional identifier string for the widget. Default is NULL.
save_button	Logical, whether to include a save button to save the chart as SVG or PNG. Default is TRUE.

Value

A GC chart widget.

Examples

genes_data <- data.frame(
  start = c(10, 50, 90, 130, 170, 210),
  end = c(40, 80, 120, 160, 200, 240),
  name = c('Gene 1', 'Gene 2', 'Gene 3', 'Gene 4', 'Gene 5', 'Gene 6'),
  group = c('A', 'A', 'B', 'B', 'A', 'C'),
  cluster = c(1, 1, 1, 2, 2, 2)
)
# Load from data.frame
GC_chart(genes_data, group = "group", cluster = "cluster", height = "200px") %>%
GC_labels("name")

# Load from a GenBank file (or a folder of .gbk files)
gbk_file <- system.file("extdata", "BGC0000001.gbk", package = "geneviewer")
GC_chart(gbk_file, height = "200px")