plotTopGenes: plotTopGenes

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

plotTopGenes

Description

plotTopGenes

Usage

plotTopGenes(se, n = 10, FDR = 0.05, diffUTR = FALSE, alpha = 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)
n	The maximum number of genes for which to plot labels
FDR	The FDR threshold above which to plot labels
diffUTR	Logical; if FALSE, uses absolute coefficients (appropriate for normal differential exon usage); if TRUE, uses non-absolute (ie changes should be in the same direction across significant bins) and width-weighted scores (i.e. larger bins have more weight) – this is relevant only when testing UTR usage.
alpha	Points transparency
...	Passed to geom_label_repel; this can for instance be used to increase 'max.overlaps' when not all desired gene labels are displayed)

Value

A ggplot

Examples

data(example_bin_se)
se <- diffSpliceWrapper(example_bin_se, ~condition)
plotTopGenes(se)

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