R/createAnnotationTrack_event.R

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

#' Create an event track from AS event
#'
#' This function creates an event track from AS event.
#'
#' @param eventGr A GRangesList object of AS event
#' @param type AS event type
#' @return an AnnotationTrack object
#' @details This function is borrowed from the \code{maser} package.
#' @references Veiga, D. (2019). maser: Mapping Alternative Splicing Events
#' to pRoteins. R package version 1.2.0. https://github.com/DiogoVeiga/maser
#' @keywords internal
#' @importFrom Gviz AnnotationTrack feature
#' @noRd
createAnnotationTrack_event <- function(eventGr, type) {
    if (type == "A3SS") {
        trackGr <- c(eventGr$exon_flanking, eventGr$exon_long,
                        eventGr$exon_flanking, eventGr$exon_short)
        trackGr$group <- rep(c("A3SS Long", "A3SS Short"), c(2, 2))
        trackGr$type <- rep("A3SS", 4)
        event_track <- AnnotationTrack(trackGr, name = "Event",
                    groupAnnotation = "group", shape = "box",
                    stacking = "squish", id = "A3SS", col = NULL,
                    col.line = NULL)
        Gviz::feature(event_track) <- rep(c("A3SS_Long", "A3SS_Short"), c(2, 2))
        return(event_track)
    }
    if (type == "A5SS") {
        trackGr <- c(eventGr$exon_long, eventGr$exon_flanking,
                        eventGr$exon_short, eventGr$exon_flanking)
        trackGr$group <- rep(c("A5SS Long", "A5SS Short"), c(2, 2))
        trackGr$type <- rep("A5SS", 4)
        event_track <- AnnotationTrack(trackGr, name = "Event",
                        groupAnnotation = "group", shape = "box",
                        stacking = "squish", id = "A5SS", col = NULL,
                        col.line = NULL)
        Gviz::feature(event_track) <- rep(c("A5SS_Long", "A5SS_Short"), c(2, 2))
        return(event_track)
    }
    if (type == "SE") {
        transcript_id <- NULL
        trackGr <- c(unlist(eventGr), unlist(eventGr[2:3]))
        trackGr$group <- rep(c("Inclusion", "Skipping"), c(3, 2))
        trackGr$type <- rep("Exon skipping", 5)
        event_track <- AnnotationTrack(trackGr, name = "Event",
                                        groupAnnotation = "group",
                                        shape = "box", stacking = "squish",
                                        id = "Exon skipping", col = NULL,
                                        col.line = NULL)
        Gviz::feature(event_track) <- rep(c("Inclusion", "Skipping"), c(3, 2))
        return(event_track)
    }
    if (type == "MXE") {
        trackGr <- c(eventGr$exon_upstream, eventGr$exon_1,
                        eventGr$exon_downstream, eventGr$exon_upstream,
                        eventGr$exon_2, eventGr$exon_downstream)
        trackGr$group <- rep(c("MXE_Exon1", "MXE_Exon2"), c(3, 3))
        trackGr$type <- rep("Mutually Exclusive Exons", 3)
        event_track <- AnnotationTrack(trackGr, name = "Event",
                                        groupAnnotation = "group",
                                        shape = "box", stacking = "squish",
                                        id = "Mutually Exclusive Exons",
                                        col = NULL, col.line = NULL)
        Gviz::feature(event_track) <- rep(c("MXE_Exon1", "MXE_Exon2"), c(3, 3))
        return(event_track)
    }
    if (type == "RI") {
        transcript_id <- NULL
        trackGr <- c(eventGr$exon_ir, eventGr$exon_upstream,
                        eventGr$exon_downstream)
        trackGr$group <- rep(c("Retention", "Non-retention"), c(1, 2))
        trackGr$type <- rep("Intron retention", 3)
        event_track <- AnnotationTrack(trackGr, name = "Event",
                                        groupAnnotation = "group",
                                        shape = "box", stacking = "squish",
                                        id = "Intron retention",
                                        col = NULL, col.line = NULL)
        Gviz::feature(event_track) <- rep(c("Retention", "Non_Retention"),
                                            c(1, 2))
        return(event_track)
    }
}