plotCoverage {SGSeq} | R Documentation

## Plot read coverage and splice junction read counts

### Description

Plot read coverage and splice junction read counts for an individual sample or averaged across samples.

### Usage

    plotCoverage(x, geneID = NULL, geneName = NULL, eventID = NULL,
      which = NULL, sample_info = NULL, sizefactor = NA, toscale = c("exon",
      "none", "gene"), color = "darkblue", ylim = NULL, label = NULL,
      nbin = 200, summary = mean, curvature = 1, main = NULL,
      min_anchor = 1, cores = 1)

### Arguments

`x` | `SGFeatureCounts` or `SGFeatures` object. If `x` is an `SGFeatureCounts` object that includes multiple samples, average coverage and splice junction counts are obtained.
`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`
`sample_info` | Data frame with sample information. If `x` is an `SGFeatureCounts` object, sample information is obtained from `colData(x)`. If `sample_info` includes multiple samples, average coverage and splice junction counts are obtained.
`sizefactor` | Numeric vector with length equal to the number of samples in `sample_info`. Used to scale coverages and splice junction counts before plotting, or before averaging across samples. Set to `NA` to disable scaling. If `NULL`, size factors are calculated as the number of bases sequenced (the product of library size and average number of bases sequenced per read or fragment), plotted coverages and splice junction counts are per 1 billion sequenced bases.
`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).
`color` | Color used for plotting coverages
`ylim` | Numeric vector of length two, determining y-axis range used for plotting coverages.
`label` | Optional y-axis label
`nbin` | Number of bins for plotting coverages
`summary` | Function used to calculate per-bin coverage summaries
`curvature` | Numeric determining curvature of plotted splice junctions.
`main` | Plot title
`min_anchor` | Integer specifiying minimum anchor length
`cores` | Number of cores available for parallel processing.

### Value

`data.frame` with information on splice junctions included in the splice graph

### Author(s)

Leonard Goldstein

### Examples

    ## Not run:
    par(mfrow = c(4, 1))
    for (j in seq_len(4)) plotCoverage(sgfc_pred[, j])

    ## End(Not run)
    NULL

[Package SGSeq version 1.20.0 Index]