plotRegions {srnadiff} | R Documentation

## Plot the coverage information surrounding genomic regions

### Description

This function plot the coverage information surrounding genomic regions while summarizing the annotation.

### Usage

    plotRegions(
      object,
      region,
      normCvg = TRUE,
      annot = NULL,
      allSignReg = TRUE,
      featureAnnot = NULL,
      flankReg = 10,
      colGroup = c("#0080ff", "#ff00ff"),
      fillReg = c("darkgreen", "darkred"),
      fillAnnot = "#FFD58A",
      type = "a",
      chrTitle = TRUE,
      trNames = c("DER", "coverage"),
      legend = TRUE,
      ...
    )

### Arguments

`object` | An object of class `srnadiffExp` as returned by `srnadiff` function.
`region` | A `GRanges` object. By example, ranges in the output from `regions` used on an object of class `srnadiffExp`.
`normCvg` | Boolean. If `TRUE` (the default), normalized coverages are displayed, else, the raw coverages are used.
`annot` | A `GRanges` or `data.frame` object containing gene and/or sRNA annotation information.
`allSignReg` | Boolean. If `TRUE`, all differeltially expressed regions contained in the annotated regions will be displayed.
`featureAnnot` | Character scalar. Feature annotation to be used, it will be one from column names of `mcols(annot)` if `annot` is a `GRanges` or one from `colnames(annot)` if `annot` is a `data.frame`.
`flankReg` | Integer value. If `flankReg` is positive, the displayed genomic interval is extended by `flankReg` nucleotides from the minimum `start` and maximum `end` from the displayed (ranges) regions.
`colGroup` | Character vector of length 2. The fill colors to be used to indicate samples per group.
`fillReg` | Character vector of length 2. The fill colors to be used to indicate 'up' or 'down' regulated regions.
`fillAnnot` | Character scalar. The fill color to be used for annotated regions.
`type` | Character vector. The plot type, one of (`"a", "l", "p", "b", "confint"`) or combinations thereof. See Details for more information on the individual plotting types.
`chrTitle` | Boolean or character vector of length one. Defaults `TRUE`, the chromosome name is added to the plot. If character, this will be used for title.
`trNames` | Title for the tracks. By default `"DER"` and `"coverage"`.
`legend` | Boolean triggering the addition of a legend to the (coverage) data track to indicate groups.
`...` | Additional display parameters to control the look and feel of the plots. See the "Display Parameters" section for functions `GenomeAxisTrack`, `GeneRegionTrack`, `AnnotationTrack`, `DataTrack` in the `Gviz` package.

### Details

This function provides a flexible genomic visualization framework by displaying tracks in the sense of the `Gviz` package. Given a region (or regions), four separate tracks are represented: (1) `GenomeAxisTrack`, a horizontal axis with genomic coordinate tickmarks for reference location to the displayed genomic regions; (2) `GeneRegionTrack`, if the `annot` argument is passed, a track displaying all gene and/or sRNA annotation information in a particular region; (3) `AnnotationTrack`, regions are plotted as simple boxes if no strand information is available, or as arrows to indicate their direction; and (4) `DataTrack`, plot the sample coverages surrounding the genomic regions.

The sample coverages can be plotted in various different forms as well as combinations thereof. Supported plotting types are:

  `p:` simple dot plot.

  `l:` lines plot.

  `b:` combination of dot and lines plot.

  `a:` lines plot of the sample-groups average (i.e., mean) values.

  `confint:` confidence intervals for average values. In combination with `a` type.

### Value

A list of GenomeGraph track objects, all inheriting from class `GdObject`.

### Examples

    srnaExp <- srnadiffExample()
    srnaExp <- srnadiff(srnaExp)

    plotRegions(srnaExp, regions(srnaExp)[1])
    plotRegions(srnaExp, regions(srnaExp)[1], type = c("a", "confint"))

[Package srnadiff version 1.14.0 Index]