geneviewer (version 0.1.10)

GC_chart: Create a GC Chart Visualization

Description

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
)

Value

A GC chart widget.

Arguments

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. Default is TRUE.

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 folder containing .gbk files
# file_path <- "~/path/to/folder/"
# GC_chart(file_path) %>%