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
)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.
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) %>%