pipe.PlotSNP: Plot Single Nucleotide Polymorphism (SNP) Sites at Nucleotide...

Description Usage Arguments Details Value Note Author(s) See Also

Description

Plot aligned read base call distributions for one or more SNP sites from one or more samples, and optionally save them as PNG images.

Usage

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pipe.PlotSNP(sampleIDs, seqID, position, geneID = NULL, groups = sampleIDs, 
		annotationFile = "Annotation.txt", optionsFile = "Options.txt", results.path = NULL, 
		tailWidth = NULL, plotFormat = c("", "png", "pdf"), plotFileName = NULL, 
		plot.path = "SNP_Plots", label = "", SNPtablePath = "~/SNPs/", mf = NULL, 
		start = NULL, stop = NULL, verbose = TRUE, ...)

Arguments

sampleIDs

A vector or one or more SampleIDs.

seqID

Character string of one chromosome name.

position

Integer vector of one or more chromosomal locations, in nucleotides.

geneID

Optional, give the GeneID of the one SNP site (just to save time).

groups

Character vector of group identifiers, of the same length as sampleIDs, used in the plot headers to show sample grouping information when making multi-sample plots.

annotationFile

The file of sample annotations.

optionsFile

The file of program options.

results.path

The folder of pipeline results, to find existing BAM files for extracting read pileup details.

tailWidth

Integer number of extra nucleotides of context, to include in the SNP plot image on both sides of the one center position of interest. There is a tradeoff between showing so much context that no SNPs are discernable, and showing so little context that the overall alignment quality in the area cannot be assured. Further, the plot function lays down so many extra supporting features that it is very hard to keep all content clear and distinct. Adjusting the tail width can help find the optimal tradeoff between clear details and adequate context.

plotFormat

Controls the plotting behaviour. Default is to write to the current graphics device. Optionally it can create PNG or PDF files on disk, using the name of the gene and nucleotide position as the default filename.

plotFileName

Optional character string of the filename to use for the created plot image file.

plot.path

Folder to write PNG or PDF image files to.

label

Optional vector of text, same length as sampleIDs, for adding to plot headers.

SNPtablePath

Pathname to optional tables of known SNP sites for this chromosome, for annotating the lower margin of the SNP plot with previously identified known SNP sites. (this functionality is only available for some organisms, and how it's implemented varies with the size of the genome...).

mf

An optional vector of length 2, as used by graphics parameters mfcol, mfrow, to control the layout of composite SNP plots that show 2 or more plots. A default layout is chosen based on the number of plots to be made, but finer control can give a more informative plot layout by careful ordering of the sample IDs and explicitly setting 'mf'.

start
stop

Optional explicit boundaries, in nucleotide units, of the region around the center SNP site to plot. Overrides tailWidth.

...

Other arguments to be passed to the low level SNP plot function.

Details

This function gives a simpler interface wrapper to the lower level SNP plot function, handling all details about SpeciesIDs, BAM files, etc.; as well as accomodating getting multiple SNP plot images into one single composite plot, as for comparing between samples.

Value

If plotFormat is not empty, then PNG or PDF files are written to disk. Otherwise creates a SNP plot image in the current graphics device.

Note

Showing SNP read pileup images for many samples at one time is quite slow, as it consumes lots of memory and time reading from multible BAM files. When the number of samples gets large, the available resolution per sample gets so small that making usable images becomes impossible.

Author(s)

Bob Morrison

See Also

pipe.PlotGene for aligned read plot images that show the depth of read coverage over entire genes, in one or more samples.


robertdouglasmorrison/DuffyNGS documentation built on Dec. 14, 2018, 3:04 p.m.