deuBinPlot {diffUTR} | R Documentation

## deuBinPlot

### Description

deuBinPlot

### Usage

    deuBinPlot(
      se,
      gene,
      type = c("summary", "condition", "sample"),
      intronSize = 2,
      exonSize = c("sqrt", "linear", "log"),
      y = NULL,
      condition = NULL,
      size = "type",
      lineSize = 1,
      colour = NULL,
      alpha = NULL,
      removeAmbiguous = TRUE,
      minDensityRatio = 0.1
    )

### Arguments

`se` | A bin-wise SummarizedExperiment as produced by `countFeatures` and including bin-level tests (i.e. having been passed through one of the DEU wrappers such as `diffSpliceWrapper` or `DEXSeqWrapper`)
`gene` | The gene of interest
`type` | Either 'summary' (plot DEU summary), 'sample' (plot sample-wise data), or 'condition' (plot data aggregate by condition)
`intronSize` | Intron plot size. If <=3, intron size will be this fraction of the mean exon size. If >3, each intron will have the given size.
`exonSize` | Scaling for exon sizes, either 'sqrt', 'log', or 'linear'.
`y` | Value to plot on the y-axis. If 'type="summary"', this should be a column of 'rowData(se)', otherwise should be an assay name of 'se'.
`condition` | The colData column containing the samples' condition.
`size` | rowData variable to use to determine the thickness of the bins.
`lineSize` | Size of the line connecting the bins. Use 'lineSize=0' to omit the line.
`colour` | rowData variable to use to determine the colour of the bins. If 'type="condition"', can also be "condition"; if 'type="sample"' can be any colData column.
`alpha` | Alpha level, passed to ggplot.
`removeAmbiguous` | Logical; whether to remove bins that are gene-ambiguous (i.e. overlap multiple genes).
`minDensityRatio` | Minimum ratio of read density (with respect to the gene's average) for a bin to be plotted.

### Value

A ggplot object

### Examples

    data(example_bin_se)
    se <- diffSpliceWrapper(example_bin_se, ~condition)
    deuBinPlot(se, "Jund")

[Package diffUTR version 1.0.0 Index]