plotSpliceGraph {SGSeq} | R Documentation

## Plot splice graph

### 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

    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

    ## 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

[Package SGSeq version 1.21.9 Index]