RAM (version 1.2.1.3)

seq_var: Plot Intra And Inter Specific Variation For An Alignment

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

Value

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

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.

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)