plotUMI4C: Plot UMI4C data

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

Plot UMI4C data

Description

Produce a UMI-4C data plot containing the genes in the region, the adaptative smoothen trend and the domainogram.

Usage

plotUMI4C(
  umi4c,
  grouping = "condition",
  dgram_function = "quotient",
  dgram_plot = 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, 0.4, 0.12, 0.23),
  font_size = 14
)

Arguments

umi4c	UMI4C object as generated by makeUMI4C.
grouping	Grouping used for the different samples. If none available or want to add new groupings, run addGrouping.
dgram_function	Function used for calculating the fold-change in the domainogram plot, either "difference" or "quotient". Default: "quotient".
dgram_plot	Logical indicating whether to plot the domainogram. If the UMI4C object only contains one sample will be automatically set to FALSE. 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

Produces a summary plot with all the information contained in the UMI4C opject.

Examples

data("ex_ciita_umi4c")
ex_ciita_umi4c <- addGrouping(ex_ciita_umi4c, grouping="condition")

plotUMI4C(ex_ciita_umi4c,
    dgram_plot = FALSE
)

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