SGSeq (version 1.2.2)

plotSpliceGraph: Plot splice graph

Description

Plot splice graph implied by splice junctions and exon bins.

Usage

plotSpliceGraph(x, geneID = NULL, geneName = NULL, eventID = NULL, which = NULL, toscale = c("exon", "none", "gene"), label = c("id", "name", "label", "none"), color = "gray", color_novel = color, color_alpha = 0.8, color_labels = FALSE, border = "fill", cexLab = 1, cexExon = 1, ypos = 0.5, score = NULL, score_color = "darkblue", score_ylim = NULL, score_ypos = c(0.3, 0.1), score_nbin = 400, score_summary = mean, ranges = NULL, ranges_color = "darkblue", ranges_ypos = c(0.1, 0.1), main = NULL, cexMain = 1, tx_view = FALSE, tx_dist = 0.2, tx_cex = 1, asp = 1)

Arguments

x

SGFeatures or SGVariants object

geneID

Single gene identifier used to subset x

geneName

Single gene name used to subset x

eventID

Single event identifier used to subset x

which

GRanges used to subset x

toscale

Controls which parts of the splice graph are drawn to scale. Possible values are “none” (exonic and intronic regions have constant length), “exon” (exonic regions are drawn to scale) and “gene” (both exonic and intronic regions are drawn to scale).

label

Format of exon/splice junction labels, possible values are “id” (format E1,... J1,...), “name” (format type:chromosome:start-end:strand), “label” for labels specified in elementMetadata column “label”, or “none” for no labels.

color

Color used for plotting the splice graph. Ignored if features elementMetadata column “color” is not NULL.

color_novel

Features with missing annotation are highlighted in color_novel. Ignored if features elementMetadata column “color” is not NULL.

color_alpha

Controls color transparency

color_labels

Logical indicating whether label colors should be the same as feature colors

border

Determines the color of exon borders, can be “fill” (same as exon color), “none” (no border) or a valid color name

cexLab

Scale factor for feature labels

cexExon

Scale factor for exon height

ypos

Numeric value indicating vertical position of splice graph (exon bins) specified as fraction of height of the plotting region (not supported for tx_view = TRUE)

score

RLeList containing nucleotide-level scores to be plotted with the splice graph

score_color

Color used for plotting scores

score_ylim

y-axis range used for plotting scores

score_ypos

Numeric vector of length two, indicating the vertical position and height of the score panel, specificed as fraction of the height of the plotting region

score_nbin

Number of bins for plotting scores

score_summary

Function used to calculate per-bin score summaries

ranges

GRangesList to be plotted with the splice graph

ranges_color

Color used for plotting ranges

ranges_ypos

Numeric vector of length two, indicating the vertical position and height of the ranges panel, specificed as fraction of the height of the plotting region

main

Plot title

cexMain

Scale factor for plot title

tx_view

Plot transcripts instead of splice graph (experimental)

tx_dist

Vertical distance between transcripts as fraction of height of plotting region

tx_cex

Scale factor for transcript labels

asp

Aspect ratio of graphics region

Value

data.frame with information on exon bins and splice junctions included in the splice graph

Details

By default, the color of features in the splice graph is determined by annotation status (see arguments color, color_novel) and feature labels are generated automatically (see argument label). Alternatively, colors and labels can be specified via elementMetadata columns “color” and “label”, respectively.

A data.frame with information on plotted features, including genomic coordinates, is returned invisibly.

Examples

## Not run: 
# sgf_annotated <- annotate(sgf, txf)
# plotSpliceGraph(sgf_annotated)
# ## End(Not run)
## Not run: 
# sgv_annotated <- annotate(sgv, txf)
# plotSpliceGraph(sgv_annotated)
# ## End(Not run)