plotTranscripts: Quickly plot transcript structure without read coverage...

In kauralasoo/wiggleplotr: Make read coverage plots from BigWig files

Quickly plot transcript structure without read coverage tracks

Description

Quickly plot transcript structure without read coverage tracks

Usage

plotTranscripts(
  exons,
  cdss = NULL,
  transcript_annotations = NULL,
  rescale_introns = TRUE,
  new_intron_length = 50,
  flanking_length = c(50, 50),
  connect_exons = TRUE,
  transcript_label = TRUE,
  region_coords = NULL
)

Arguments

exons	list of GRanges objects, each object containing exons for one transcript. The list must have names that correspond to transcript_id column in transript_annotations data.frame.
cdss	list of GRanges objects, each object containing the coding regions (CDS) of a single transcript. The list must have names that correspond to transcript_id column in transript_annotations data.frame. If cdss is not specified then exons list will be used for both arguments. (default: NULL)
transcript_annotations	Data frame with at least three columns: transcript_id, gene_name, strand. Used to construct transcript labels. (default: NULL)
rescale_introns	Specifies if the introns should be scaled to fixed length or not. (default: TRUE)
new_intron_length	length (bp) of introns after scaling. (default: 50)
flanking_length	Lengths of the flanking regions upstream and downstream of the gene. (default: c(50,50))
connect_exons	Print lines that connect exons together. Set to FALSE when plotting peaks (default: TRUE).
transcript_label	If TRUE then transcript labels are printed above each transcript. (default: TRUE).
region_coords	Start and end coordinates of the region to plot, overrides flanking_length parameter.

Value

ggplot2 object

Examples

plotTranscripts(ncoa7_exons, ncoa7_cdss, ncoa7_metadata, rescale_introns = FALSE)

kauralasoo/wiggleplotr documentation built on July 4, 2022, 11:43 a.m.