viewTranscripts: Plot transcripts directly from GTF.

In fursham-h/factR: Functional Annotation of Custom Transcriptomes

Plot transcripts directly from GTF.

Description

A wrapper around wiggleplotr's plotTranscripts function. See the documentation for (plotTranscripts) for more information.

Usage

viewTranscripts(x, ..., rescale_introns = FALSE, ncol = 1)

Arguments

x	GRanges object containing transcript annotation in GTF format
...	Character value of features to plot. Multiple features can be plotted by entering comma-delimited values. Features will be extracted from metadata gene_name, gene_id and transcript_id of the GTF. Can also be a conditional statement to filter values from variables in the GTF (e.g. gene_name == "Ptbp1")
rescale_introns	Specifies if the introns should be scaled to fixed length or not. (default: FALSE)
ncol	Number of columns to patch the output plots (default: 1)

Value

ggplot2 object. If multiple genes are detected, plots will be combined using patchwork

Author(s)

Fursham Hamid

Examples

## ---------------------------------------------------------------------
## EXAMPLE USING SAMPLE DATASET
## ---------------------------------------------------------------------
# Load datasets
data(query_gtf, ref_gtf)

viewTranscripts(query_gtf)
viewTranscripts(query_gtf, "transcript1")
viewTranscripts(ref_gtf)

## ---------------------------------------------------------------------
## EXAMPLE USING TRANSCRIPT ANNOTATION
## ---------------------------------------------------------------------

library(AnnotationHub)

## Retrieve GRCm38 trancript annotation
ah <- AnnotationHub()
GRCm38_gtf <- ah[["AH60127"]]

## Plot transcripts from Ptbp1 gene
viewTranscripts(GRCm38_gtf, "Ptbp1")

# Plot transcripts from Ptbp1 and Ptbp2 genes
viewTranscripts(GRCm38_gtf, "Ptbp1", "Ptbp2")

fursham-h/factR documentation built on Aug. 20, 2023, 1:58 p.m.