geneBinHeatmap {diffUTR} | R Documentation

## geneBinHeatmap

### Description

A wrapper around 'ComplexHeatmap'.

### Usage

    geneBinHeatmap(
      se,
      gene,
      what = NULL,
      anno_rows = c("type", "logWidth", "meanLogDensity", "log10PValue", "geneAmbiguous"),
      anno_columns = c(),
      anno_colors = list(),
      removeAmbiguous = FALSE,
      merge_legends = TRUE,
      cluster_columns = FALSE,
      minDensityRatio = 0.1,
      left_annotation = NULL,
      top_annotation = NULL,
      ...
    )

### Arguments

`se` | A bin-wise SummarizedExperiment as produced by `countFeatures`
`gene` | The gene of interest
`what` | Type of values (i.e. assay) to plot
`anno_rows` | Row annotation columns (i.e. columns of 'rowData(se)') to plot
`anno_columns` | Column annotation columns (i.e. columns of 'colData(se)') to plot
`anno_colors` | Annotation colors, as a list named with the row/column annotations, see '`SingleAnnotation`' for details. Ignored if 'left_annotation' and/or 'top_annotation' are given directly.
`removeAmbiguous` | Logical; whether to remove bins that are gene-ambiguous (i.e. overlap multiple genes).
`merge_legends` | Logical; whether to merge legends. This effectively calls 'draw(..., merge_legends=TRUE)' around the heatmap.
`cluster_columns` | Logical; whether to cluster columns (passed to `Heatmap`)
`minDensityRatio` | Minimum ratio of read density (with respect to the gene's average) for a bin to be plotted.
`left_annotation` | Passed to `Heatmap`, overrides 'anno_rows'.
`top_annotation` | Passed to `Heatmap`, overrides 'anno_columns'.
`...` | Passed to 'ComplexHeatmap' (see `Heatmap`)

### Value

A `Heatmap`

### Examples

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

[Package diffUTR version 1.0.0 Index]