R: Plot genotype frequencies of regions across datasets.
plotGenotypesPerSNP
R Documentation
Plot genotype frequencies of regions across datasets.
Description
Creates bar plots for the distribution of genotype frequencies of regions across individuals.
Usage
plotGenotypesPerSNP(SNPhood.o, regions = NULL, fileToPlot = NULL,
verbose = FALSE)
Arguments
SNPhood.o
Object of class SNPhood
regions
Numeric or Character or NULL. Default NULL. Regions that should be plotted, either specified as integer (such as 1, value must be
between 1 and the total number of regions as defined in the object) or their annotation (name must appear in the region names as obtained via the function annotationRegions). If set to NULL, all regions will be considered.
fileToPlot
Character(1) or NULL. Default NULL.
Filename of the PDF file for the output plots.
If set to NULL, plots will be plotted to the currently active device.
verbose
Logical(1). Default FALSE. Should the verbose mode (i.e., diagnostic messages during execution of the script) be enabled?
Value
the generated ggplot2 plot(s) as list for further processing. May contain multiple plots, depending on the function. The plot(s) can then be plotted individually or modified arbitrarily as the user wants. For example, if multiple plots are returned and the plots have been saved in a variable called plots.l, simply type plots.l[[1]] to view the first plot.
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(SNPhood)
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: data.table
Attaching package: 'data.table'
The following object is masked from 'package:GenomicRanges':
shift
The following object is masked from 'package:IRanges':
shift
Loading required package: checkmate
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| Welcome to the SNPhood package and thank you for using our software. This is SNPhood version 1.2.2. |
| See the vignettes (type browseVignettes("SNPhood") or the help pages for how to use SNPhood for your analyses. |
| Thank you for using our software. Please do not hesitate to contact us if there are any questions. |
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> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/SNPhood/plotGenotypesPerSNP.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotGenotypesPerSNP
> ### Title: Plot genotype frequencies of regions across datasets.
> ### Aliases: plotGenotypesPerSNP
>
> ### ** Examples
>
> data(SNPhood.o, package="SNPhood")
> plot = plotGenotypesPerSNP(SNPhood.o, regions=1:20)
Cannot display 4 SNP genotypes because all genotypes were NA. Remaining number of SNPs to display: 16
>
>
>
>
>
> dev.off()
null device
1
>
providing 
.