plotMiR: Plot miRNA analysis results

In Aufiero/circRNAprofiler: circRNAprofiler: An R-Based Computational Framework for the Downstream Analysis of Circular RNAs

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

Aufiero/circRNAprofiler documentation built on Nov. 3, 2024, 10:12 a.m.