visualize: AS event and pathway visualization

In nachoryu/ASpediaFI: ASpedia-FI: Functional Interaction Analysis of Alternative Splicing Events

AS event and pathway visualization

Description

Visualize AS event or pathway. If an AS event node is given, the function modified from the plotTranscripts function in the maser package is used to visualize the event. If a pathway node is given, a subnetwork pertaining to the pathway is visualized.

Usage

visualize(object, node, zoom = NULL, n = NULL)

Arguments

object	Object of class ASpediaFI
node	the name of AS event or pathway
zoom	a logical to determine if genomic coordinates are zoomed (for AS event visualization)
n	the number of genes and AS events to be shown (for pathway visualization)

Value

a plot demonstrating AS event or pathway

References

Veiga, D. (2019). maser: Mapping Alternative Splicing Events to pRoteins. R package version 1.2.0. https://github.com/DiogoVeiga/maser

Examples

## Not run: 
# Visualize AS event
visualize(GSE114922.ASpediaFI,
    node = as.table(GSE114922.ASpediaFI)$EventID[1],
    zoom = FALSE
)

# Visualize pathway
visualize(GSE114922.ASpediaFI, node = 'HALLMARK_HEME_METABOLISM', n = 10)

## End(Not run)

nachoryu/ASpediaFI documentation built on Aug. 19, 2022, 7:51 a.m.