plotHisto: Plot a histogram of the data values

In RNAither: Statistical analysis of high-throughput RNAi screens

Description

Plots and saves a histogram of the chosen data values.

Usage

plotHisto(header, dataset, channel, plotTitle, showPlot)

Arguments

header	the header of a dataset file generated with generateDatasetFile
dataset	an R data frame generated with generateDatasetFile
channel	a character string specifying the name of the column containing the values to be plotted, e.g. "SigIntensity"
plotTitle	the plot title
showPlot	0 or 1. 1 will open one or several plot windows in the R GUI, 0 will only save the plot(s) without opening windows.

Value

Saves the histogram in a pdf and a png file named after the experiment name specified in the header concatenated with the plotTitle.

The function returns the plot name.

See Also

plotHistoPerplate, plotHistoPerscreen

Examples

data(exampleHeader, package="RNAither")
data(exampleDataset, package="RNAither")

plotHisto(header, dataset, "SigIntensity", "Distribution of Data and Controls", 1)

Example output

Loading required package: topGO
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, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, 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,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: graph
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: GO.db
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    expand.grid


Loading required package: SparseM

Attaching package: 'SparseM'

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

    backsolve


groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.

Attaching package: 'topGO'

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

    members

Loading required package: RankProd
Loading required package: Rmpfr
Loading required package: gmp

Attaching package: 'gmp'

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

    %*%, apply, crossprod, matrix, tcrossprod

C code of R package 'Rmpfr': GMP using 64 bits per limb


Attaching package: 'Rmpfr'

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

    outer

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

    cbind, pmax, pmin, rbind

The following objects are masked from 'package:S4Vectors':

    cbind, rbind

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

    cbind, pmax, pmin, rbind

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

    dbinom, dnorm, dpois, pnorm

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

    cbind, pmax, pmin, rbind

Loading required package: prada
Loading required package: RColorBrewer
Loading required package: grid

Attaching package: 'grid'

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

    depth

Loading required package: rrcov
Loading required package: robustbase

Attaching package: 'robustbase'

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

    rowMedians

Scalable Robust Estimators with High Breakdown Point (version 1.4-7)


Attaching package: 'RNAither'

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

    trim

RNAither documentation built on Nov. 8, 2020, 8:06 p.m.