seq_var: Plot Intra And Inter Specific Variation For An Alignment

In RAM: R for Amplicon-Sequencing-Based Microbial-Ecology

Description

This function calculates and plots inter- and intra- specific variation for an alignment.

Usage

seq_var(taxon=NULL, region="ITS", align=NULL, file.align=NULL,
        file.align.format="fasta", outgroup.name=NULL,
        taxa.sep=":", col.total=5, col.genus=1, 
        col.genus.syn=3, col.species=4, col.strain=5,
        box.cex.axis.text.x=6, box.cex.axis.text.y=6,
        box.cex.xlab=8, box.cex.ylab=8,
        intra.fill="purple", inter.fill="orange",
        den.cex.axis.text.x=6, den.cex.axis.text.y=6,
        den.cex.xlab=6, den.cex.ylab=6, frame.col="blue",
        table.cex=8, main=FALSE, main.cex=14,
        file=NULL, width=8, height=8)

Arguments

taxon	the name of the genus to be analyzed.
region	the DNA region of the alignment
align	optional, an alignment object in R environment
file.align	optional, a file of an alignment
file.align.format	alignment file format, default is in FASTA format
outgroup.name	the genus/genera names
taxa.sep	the separator used to split alignment ID, default is ':'. e.g. genus_name:seq_identifier:genus_synonym:species:strain
col.total	using the taxa.sep, how many columns the alignment ID can be split in to.
col.genus	genus name location
col.genus.syn	generic synonyms location
col.species	species name location
col.strain	strain information location
box.cex.axis.text.x	size of labels on x-axis of the boxplots
box.cex.axis.text.y	size of labels on y-axis of the boxplot
box.cex.xlab	size of the xlab of boxplots
box.cex.ylab	size of ylab of boxplots,
intra.fill	color to fill the intra specific variation boxplot and density plot. Default is "purple".
inter.fill	color to fill the intra specific variation boxplot and density plot. Default is "orange",
den.cex.axis.text.x	size of labels on x-axis of the density plots
den.cex.axis.text.y	size of labels on y-axis of the density plots
den.cex.xlab	size of the xlab of density plots
den.cex.ylab	size of the ylab of boxplots
frame.col	color of the frames separating inter- and intra-specific variation plots and tables
table.cex	the font size of the summary table
main	whether or not to give a title to the plot, can be "FALSE", "TRUE", or a string
main.cex	font size of the title of the plot
file	whether or not save the plot to a PDF file.
width	width of the plot
height	height of the plot

Details

The sequence ID of the alignment to be analyzed should be in a similar format as follows: Alternaria:gb_AF229477:Bipolaris:tetramera:strain_BMP_51_31_01, the separator, ':', and the location of genus/species/strain names can be changes or rearranged, as long as you provide such information to the function properly.

Value

This function calculate and plot inter/intra specific variation for an alignment.

Author(s)

Wen Chen & C. Andre Levesque

Examples

data(alignment)
## Not run: 
seq_var(taxon="Claviceps", region="ITS", align=alignment,
        file.align=NULL, outgroup.name=c("Talaromyces"),
        box.cex.axis.text.x=6, box.cex.axis.text.y=6, 
        box.cex.xlab=8, box.cex.ylab=8, intra.fill="purple", 
        inter.fill="orange", den.cex.axis.text.x=6, 
        den.cex.axis.text.y=6, den.cex.xlab=6, den.cex.ylab=6, 
        table.cex=8, frame.col="blue", main=TRUE, main.cex=14)
seq_var(taxon="Claviceps", region="ITS", align=NULL,
        file.align="/path/to/alignment_file", 
        outgroup.name=c("Talaromyces"), box.cex.axis.text.x=6, 
        box.cex.axis.text.y=6, box.cex.xlab=8,
        box.cex.ylab=8, intra.fill="purple", 
        inter.fill="orange", den.cex.axis.text.x=6, 
        den.cex.axis.text.y=6, den.cex.xlab=6, den.cex.ylab=6, 
        table.cex=8, frame.col="blue", main=TRUE, main.cex=14)

## End(Not run)

RAM documentation built on May 2, 2019, 3:04 p.m.