plot_features {Rgff}

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)