plotPromoters {proActiv} | R Documentation

## Visualizes promoter activity and transcript model for a gene of interest

### Description

Visualizes promoter activity and transcript model for a gene of interest

### Usage

    plotPromoters(
      result,
      gene,
      txdb,
      ranges,
      cex.title = 0.9,
      cex.axis = 0.9,
      cex.main = 1,
      blk.width = 500,
      blk.fill = "grey",
      blk.border = "darkgrey",
      label.col = "black",
      label.size = 0.7,
      arrow.width = NULL,
      arrow.fill = "transparent",
      arrow.border = "grey"
    )

### Arguments

`result` | A SummarizedExperiment object with assays giving promoter counts,activity and gene expression and promoter gene id mapping stored as row data
`gene` | A character vector of length 1. Single gene of interest to be plotted
`txdb` | A TxDb object. The txdb must correspond to the genome version used in running proActiv. Here, it is recommended to use the same txdb in generating promoter annotations
`ranges` | A list of GRanges. Each entry in the list should correspond to a transcript that will be visualized, with Genomic Ranges giving the exons corresponding to that transcript
`cex.title` | A numeric value. Size of axis labels. Defaults to 0.9
`cex.axis` | A numeric value. Size of axis and axis ticks. Defaults to 0.9
`cex.main` | A numeric value. Size of plot name. Defaults to 1
`blk.width` | A numeric value. The width of promoters blocks in the data track. Defaults to 500 (bases)
`blk.fill` | A character vector of length 1. The fill colour of the promoter blocks in the data track. Defaults to 'grey'
`blk.border` | A character vector of length 1. The border colour of the promoter blocks in the data track. Defaults to 'darkgrey'
`label.col` | A character vector of length 1. The font colour of the promoter ID label in the annotation track. Defaults to 'black'
`label.size` | A numeric value. The size of the promoter ID label in the annotation track. Defaults to 0.7
`arrow.width` | A numeric value. The width of promoter arrows in the annotation track. This value is internally calculated based on the gene of interest
`arrow.fill` | A character vector of length 1. The fill colour of the promoter arrows in the annotation track. Defaults to 'transparent'
`arrow.border` | A character vector of length 1. The border colour of the promoter arrows in the annotation track. Defaults to 'grey'

### Value

Outputs a plot of the promoters of the gene of interest across conditions, along with a model of transcripts belonging to the gene

### Examples

    ## First, run proActiv to generate a summarizedExperiment result
    files <- list.files(system.file('extdata/vignette/junctions',
                          package = 'proActiv'),
                          full.names = TRUE)
    promoterAnnotation <- promoterAnnotation.gencode.v34.subset
    result <- proActiv(files = files,
                           promoterAnnotation  = promoterAnnotation,
                           condition = rep(c('A549','HepG2'), each=3),
                           ncores = 1)
    ## Read in pre-computed ranges
    txdb <- AnnotationDbi::loadDb(system.file('extdata/vignette/annotations',
                                      'gencode.v34.annotation.rap1gap.sqlite',
                                      package = 'proActiv'))
    ## Declare a gene of interest
    gene <- 'ENSG00000076864.19'
    ## Call plot
    plotPromoters(result = result, gene = gene, txdb = txdb)

[Package proActiv version 1.2.0 Index]