Plot the amount of isomiRs in different samples

Description

This function plot different isomiRs proportion for each sample. It can show trimming events at both side, additions and nucleotides changes.

Usage

isoPlot(ids, type = "iso5", column = "condition")

Arguments

Details

There are four different values for type parameter. To plot trimming at 5' or 3' end, use type="iso5" or type="iso3". In this case, it will plot 3 positions at both side of the reference position described at miRBase site. Each position refers to the number of sequences that start/end before or after the miRBase reference. The color indicates the sample group. The size of the point is proportional to the number of total counts. The position at y is the number of different sequences.

Same logic applies to type="add" and type="subs". However, when type="add", the plot will refer to addition events from the 3' end of the reference position. Note that this additions don't match to the precursor sequence, they are non-template additions. In this case, only 3 positions after the 3' end will appear in the plot. When type="subs", it will appear one position for each nucleotide in the reference miRNA. Points will indicate isomiRs with nucleotide changes at the given position.

Value

ggplot object showing different isomiRs changes at different positions.

Examples

data(mirData)
isoPlot(mirData)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(isomiRs)
Loading required package: DiscriMiner
Loading required package: IRanges
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/isomiRs/isoPlot.Rd_%03d_medium.png", width=480, height=480)
> ### Name: isoPlot
> ### Title: Plot the amount of isomiRs in different samples
> ### Aliases: isoPlot
> 
> ### ** Examples
> 
> data(mirData)
> isoPlot(mirData)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>