This function plot different isomiRs proportion for each sample at a given
position focused on the nucleotide change that happens there.
Usage
isoPlotPosition(ids, position = 1, column = "condition")
Arguments
ids
object of class IsomirDataSeq
position
integer indicating the position to show
column
string indicating the column in
colData to color samples.
Details
It shows the nucleotides changes at the given position for each
sample in each group.
The color indicates the sample group. The size of the point is proportional
to the number of total counts of isomiRs with changes.
The position at y is the number of different sequences
supporting the change.
Value
ggplot object showing nucleotide changes
at a given position.
Examples
data(mirData)
isoPlotPosition(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/isoPlotPosition.Rd_%03d_medium.png", width=480, height=480)
> ### Name: isoPlotPosition
> ### Title: Plot nucleotides changes at a given position
> ### Aliases: isoPlotPosition
>
> ### ** Examples
>
> data(mirData)
> isoPlotPosition(mirData)
>
>
>
>
>
> dev.off()
null device
1
>