Plotting Functions

Description

The 'plotConfidenceIntervals' is a high-level plotting function for visualizing confidence intervals. The 'plotAbundanceShift' function visualizes the shift in mismatch rates between two samples.

Usage

plotConfidenceIntervals(x, ylim = c(-1.05, 1.05), color = NULL, ...)

plotAbundanceShift(x, ylim = c(-0.05, 1.05), rates = TRUE, ...)

Arguments

Value

For a 'GRanges' input: A 'ggbio' object

For a 'data.frame' input: A 'ggplot' object

Examples

## Generate sample data
counts = data.frame(x1 = 1:5, n1 = 30, x2 = 0:4, n2 = 30)

## Agresti-Caffo
ci_ac = with(counts, acCi(x1, n1, x2, n2))

library(GenomicRanges)
gr = GRanges("1", IRanges(start = 1:nrow(counts), width = 1))
mcols(gr) = ci_ac

## GRanges
plotConfidenceIntervals(gr)

## data.frame
plotConfidenceIntervals(ci_ac)

## abundance shift
plotAbundanceShift(gr)

plotAbundanceShift(ci_ac)

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(Rariant)
Loading required package: GenomicRanges
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: IRanges
Loading required package: GenomeInfoDb
Loading required package: VariantAnnotation
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")'.

Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'VariantAnnotation'

The following object is masked from 'package:base':

    tabulate

Warning message:
replacing previous import 'ggplot2::Position' by 'BiocGenerics::Position' when loading 'ggbio' 
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/Rariant/plot-cis.rd_%03d_medium.png", width=480, height=480)
> ### Name: plotCIs
> ### Title: Plotting Functions
> ### Aliases: plotCIs plotConfidenceIntervals plotAbundanceShift
> 
> ### ** Examples
> 
> ## Generate sample data
> counts = data.frame(x1 = 1:5, n1 = 30, x2 = 0:4, n2 = 30)
> 
> ## Agresti-Caffo
> ci_ac = with(counts, acCi(x1, n1, x2, n2))
> 
> library(GenomicRanges)
> gr = GRanges("1", IRanges(start = 1:nrow(counts), width = 1))
> mcols(gr) = ci_ac
> 
> ## GRanges
> plotConfidenceIntervals(gr)
> 
> ## data.frame
> plotConfidenceIntervals(ci_ac)
> 
> ## abundance shift
> plotAbundanceShift(gr)
> 
> plotAbundanceShift(ci_ac)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>