geneBinHeatmap: geneBinHeatmap

In ETHZ-INS/diffUTR: diffUTR: Streamlining differential exon and 3' UTR usage

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")

ETHZ-INS/diffUTR documentation built on Nov. 3, 2024, 6:26 p.m.