plotUMI4C {UMI4Cats} | R Documentation

## 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
    )

[Package UMI4Cats version 1.2.1 Index]