circularfv_rjs {RJSplot}

Pruduce a circular sequence viewer.

Description

circularfv_rjs creates a circular sequence viewer.

Usage

circularfv_rjs(sequence, features = FALSE,
               plot = TRUE, jupyter = FALSE, dir = tempdir())

Arguments

sequence

a "character" string giving the DNA sequence.

features

Data Frame with the segments that will be seen in the viewer. It cotains 5 columns which describes the identifier, start coordinate, stop coordinate, segment type and segment color.

plot

open resulting graph in your browser.

jupyter

embed the graph as an iframe into a Jupyter Notebook.

dir

a "character" string representing the directory where the graph will be saved.

Value

The function creates a folder in your computer with an HTML document named index.html which contains the graph. This file can be directly opened with your browser.

Author(s)

David Barrios and Carlos Prieto. Bioinformatics Service of Nucleus, University of Salamanca. See https://bioinfo.usal.es/

See Also

The ‘RJSplot’ Website: https://rjsplot.usal.es

dendrogram_rjs, densityplot_rjs, genomemap_rjs, heatmap_rjs, manhattan_rjs, network_rjs, scatterplot_rjs, symheatmap_rjs, wordcloud_rjs, boxplot_rjs, bubbles_rjs, hiveplot_rjs, piechart_rjs, barplot_rjs, tables_rjs, surface3d_rjs, scatter3d_rjs.

Examples

if(interactive()){
## Creates a circular sequence viewer in a temporal directory of your local machine
## Generate test input data
sequence <- paste(sample(c("c","a","t","g"), 10000, replace = TRUE), collapse = "")
data <- matrix(round(runif(12,0,10000)),6,2)
features <- data.frame(id = 0:5, start = data[,1], stop = data[,2],
type = c("voluptate","non","voluptate","sit","et","proident"),
color = c("SandyBrown","Tan","Wheat","SteelBlue","LightSkyBlue","LightBlue"))

## Create the circular sequence viewver
circularfv_rjs(sequence, features)
}