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

Description Usage Arguments Value Examples

View source: R/wiggleplotr.R

Description

Quickly plot transcript structure without read coverage tracks

Usage

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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

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kauralasoo/wiggleplotr documentation built on July 21, 2021, 4:15 a.m.