plotMiR {circRNAprofiler} | R Documentation

## Plot miRNA analysis results

### Description

The function plotMiR() generates a scatter plot showing the number of miRNA binding sites for each miR found in the target sequence.

### Usage

    plotMiR(rearragedMiRres, n = 40, color = "blue", miRid = FALSE,
      id = 1)

### Arguments

`rearragedMiRres` | A list containing containing rearranged miRNA analysis results. See `getMiRsites` and then `rearrangeMiRres`.
`n` | An integer specifying the miRNA binding sites cut-off. The miRNA with a number of binding sites equals or higher to the cut-off will be colored. Deafaut value is 40.
`color` | A string specifying the color of the top n miRs. Default value is "blue".
`miRid` | A logical specifying whether or not to show the miR ids in the plot. default value is FALSE.
`id` | An integer specifying which element of the list rearragedMiRres to plot. Each element of the list contains the miR resutls relative to one circRNA. Deafult value is 1.

### Value

A ggplot object.

### Examples

    # Load data frame containing detected back-spliced junctions
    data("mergedBSJunctions")

    # Load short version of the gencode v19 annotation file
    data("gtf")

    # Annotate the first back-spliced junctions
    annotatedBSJs <- annotateBSJs(mergedBSJunctions[1, ], gtf)

    # Get genome
    genome <- BSgenome::getBSgenome("BSgenome.Hsapiens.UCSC.hg19")

    # Retrieve target sequences.
    targets <- getCircSeqs(
        annotatedBSJs,
        gtf,
        genome)

    # Screen target sequence for miR binding sites.
    pathToMiRs <- system.file("extdata", "miRs.txt", package="circRNAprofiler")

    # miRsites <- getMiRsites(
    #     targets,
    #     miRspeciesCode = "hsa",
    #     miRBaseLatestRelease = TRUE,
    #     totalMatches = 6,
    #     maxNonCanonicalMatches = 1,
    #     pathToMiRs)

    # Rearrange miR results
    # rearragedMiRres <- rearrangeMiRres(miRsites)

    # Plot
    # p <- plotMiR(
    #     rearragedMiRres,
    #     n = 20,
    #     color = "blue",
    #     miRid = TRUE,
    #     id = 3)
    # p

[Package circRNAprofiler version 1.1.0 Index]