deuBinPlot: deuBinPlot

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

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")

ETHZ-INS/diffUTR documentation built on March 18, 2023, 8:54 a.m.