plot_features: Plots or exports an image of the feature tree from a GFF file

In Rgff: R Utilities for GFF Files

Plots or exports an image of the feature tree from a GFF file

Description

This function plots the feature tree from a GFF file or, if an output file name is provided, exports an image of in the desired format ("png", "pdf" or "svg"). Packages "DiagrammeR", "DiagrammeRsvg" and "rsvg" must be installed to use this function.

Usage

plot_features(
  inFile,
  outFile,
  includeCounts = FALSE,
  fileType = c("AUTO", "GFF3", "GTF"),
  exportFormat = c("png", "pdf", "svg")
)

Arguments

inFile	Path to the input GFF file
outFile	Path to the output features image file, if not provided the tree will be plotted
includeCounts	Include number of occurrences of each subfeature
fileType	Version of the input file (GTF/GFF3). If not provided it will be determined from the file name.
exportFormat	Output image format when it is not possible to deduce it from the extension of outFile ("png", "pdf" or "svg"). Default, "png"

Value

Path of the output features image file

Examples

test_gff3<-system.file("extdata", "AthSmall.gff3", package="Rgff")
plot_features(test_gff3)

Rgff documentation built on Sept. 30, 2022, 5:08 p.m.