plotMiR {circRNAprofiler} | R Documentation |
The function plotMiR() generates a scatter plot showing the number of miRNA binding sites for each miR found in the target sequence.
plotMiR(rearragedMiRres, n = 40, color = "blue", miRid = FALSE, id = 1)
rearragedMiRres |
A list containing containing rearranged
miRNA analysis results. See |
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. |
A ggplot object.
# 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