Plot transcripts directly from GTF.

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

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

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
## ---------------------------------------------------------------------
# \donttest{
library(AnnotationHub)

## Retrieve GRCm38 trancript annotation
ah <- AnnotationHub()
#> snapshotDate(): 2022-10-31
GRCm38_gtf <- ah[["AH60127"]]
#> loading from cache
#> Importing File into R ..
#> 'getOption("repos")' replaces Bioconductor standard repositories, see
#> '?repositories' for details
#> 
#> replacement repositories:
#>     CRAN: https://cloud.r-project.org
#> 'getOption("repos")' replaces Bioconductor standard repositories, see
#> '?repositories' for details
#> 
#> replacement repositories:
#>     CRAN: https://cloud.r-project.org

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


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

# }