plotInteractionsUMI4C: Plot Interactions UMI4C

In Pasquali-lab/UMI4Cats: UMI4Cats: Processing, analysis and visualization of UMI-4C chromatin contact data

Plot Interactions UMI4C

Description

Plot the results of callInteractions together with the gene annotation and the trend.

Usage

plotInteractionsUMI4C(
  umi4c,
  gr_interactions,
  grouping = "condition",
  significant = TRUE,
  colors = NULL,
  xlim = NULL,
  ylim = NULL,
  TxDb = TxDb.Hsapiens.UCSC.hg19.knownGene::TxDb.Hsapiens.UCSC.hg19.knownGene,
  longest = TRUE,
  rel_heights = c(0.25, 0.5, 0.25),
  font_size = 14
)

Arguments

umi4c	UMI4C object as generated by makeUMI4C.
gr_interactions	GRangesList outputed by callInteractions.
grouping	Grouping used for the different samples. If none available or want to add new groupings, run addGrouping.
significant	Logical indicating whether to plot only significant interactions (default: TRUE).
colors	Named vector of colors to use for plotting for each group.
xlim	Limits for the plot x axis (genomic coordinates).
ylim	Limits of the trend y axis.
TxDb	TxDb object to use for drawing the genomic annotation.
longest	Logical indicating whether to plot only the longest transcripts for each gene in the gene annotation plot.
rel_heights	Numeric vector of length 3 or 4 (if differential plot) indicating the relative heights of each part of the UMI4C plot.
font_size	Base font size to use for the UMI4C plot. Default: 14.

Value

Combined plot with gene annotation, trend and interaction plot.

Pasquali-lab/UMI4Cats documentation built on Nov. 3, 2024, 3:10 p.m.