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Last data update: 2014.03.03

R: Graphical exploration of a specific metadata column.

plotMetaDataExpl

R Documentation

Graphical exploration of a specific metadata column.

Description

plotMetaDataExpl plots density and box-plot of an specific metadata column. If the characteristic is non numerical, then a frequency plot is built.

Usage

plotMetaDataExpl(object, name = c("length", "gc", "pool"), log = FALSE,
    join = TRUE, absolute = FALSE, color = "blue")

## S4 method for signature 'TargetExperiment'
plotMetaDataExpl(object, name = c("length", "gc",
    "pool"), log = FALSE, join = TRUE, absolute = FALSE, color = "blue")

Arguments

`object`	TargetExperiment class object.
`name`	a character indicating the metadata column name that should be analyzed.
`log`	Logical indicating if the numerical metadata column should be considered in log10 scale.
`join`	Logical only for numerical variables. It indicates if boxplot and density function should be plotted together using the ggplot2 geom_violin method.
`absolute`	Logical indicating if the frequencies of the selected categorical metadata column should be in absolute scale. If absoulte is FALSE the frequencies are in relative percentages.
`color`	A character indicating a valid name color.

Value

ggplot2 graphics.

Note

see full example in TargetExperiment-class

Author(s)

Gabriela A. Merino gmerino@bdmg.com.ar, Cristobal Fresno cfresno@bdmg.com.ar and Elmer A. Fernandez efernandez@bdmg.com.ar

Examples

## Loading the TargetExperiment object
data(ampliPanel, package="TarSeqQC")

# Attribute boxplot and density plot exploration
g<-plotMetaDataExpl(ampliPanel, name="length")
if(interactive())
{
# x11(type="cairo")
g
}
# Explore amount of amplicons per gene
g<-plotMetaDataExpl(ampliPanel, name="gene", absolute=TRUE)
if(interactive())
{
# x11(type="cairo")
g
}

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(TarSeqQC)
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: Rsamtools
Loading required package: Biostrings
Loading required package: XVector
Loading required package: ggplot2
Loading required package: plyr

Attaching package: 'plyr'

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

    compact

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

    desc

The following object is masked from 'package:S4Vectors':

    rename

Loading required package: openxlsx
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/TarSeqQC/TargetExperiment-plotMetaDataExpl.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotMetaDataExpl
> ### Title: Graphical exploration of a specific metadata column.
> ### Aliases: plotMetaDataExpl plotMetaDataExpl,TargetExperiment-method
> ###   plotMetaDataExpl-methods
> 
> ### ** Examples
> 
> ## Loading the TargetExperiment object
> data(ampliPanel, package="TarSeqQC")
> 
> # Attribute boxplot and density plot exploration
> g<-plotMetaDataExpl(ampliPanel, name="length")
> #if(interactive())
> #{
> # x11(type="cairo")
> g
> #}
> # Explore amount of amplicons per gene
> g<-plotMetaDataExpl(ampliPanel, name="gene", absolute=TRUE)
> #if(interactive())
> #{
> # x11(type="cairo")
> g
> #}
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>