plotSpliceGraph: Plot splice graph

Description Usage Arguments Details Value Author(s) Examples

View source: R/plots.R

Description

Plot the splice graph implied by splice junctions and exon bins. Invisibly returns a data.frame with details of plotted features, including genomic coordinates.

Usage

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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",
  curvature = NULL, ypos = c(0.5, 0.1), score = NULL,
  score_color = "darkblue", score_ylim = NULL, score_ypos = c(0.3, 0.1),
  score_nbin = 200, score_summary = mean, score_label = NULL,
  ranges = NULL, ranges_color = "darkblue", ranges_ypos = c(0.1, 0.1),
  main = NULL, tx_view = FALSE, tx_dist = 0.2, short_output = TRUE)

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 metadata column “label”, or “none” for no labels.

color

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

color_novel

Features with missing annotation are highlighted in color_novel. Ignored if features metadata 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

curvature

Numeric determining curvature of plotted splice junctions.

ypos

Numeric vector of length two, indicating the vertical position and height of the exon bins in the splice graph, specificed as fraction of the 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

Numeric vector of length two, determining y-axis range 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

score_label

Label used to annotate score panel

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

tx_view

Plot transcripts instead of splice graph (experimental)

tx_dist

Vertical distance between transcripts as fraction of height of plotting region

short_output

Logical indicating whether the returned data frame should only include information that is likely useful to the user

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 metadata columns “color” and “label”, respectively.

Value

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

Author(s)

Leonard Goldstein

Examples

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## Not run: 
sgf_annotated <- annotate(sgf_pred, txf_ann)
plotSpliceGraph(sgf_annotated)

## End(Not run)
## Not run: 
sgv_annotated <- annotate(sgv_pred, txf_ann)
plotSpliceGraph(sgv_annotated)

## End(Not run)
NULL

ldg21/SGSeq documentation built on May 7, 2019, 9:37 a.m.