refpkg: Summary data and plots for reference packages

In BoSSA: A Bunch of Structure and Sequence Analysis

Description

Summary data and plots for reference packages

Usage

refpkg(refpkg_path,type="summary",rank_tree="species",
rank_pie=c("phylum","class","order","family","genus"),
scale_pie=TRUE,alpha_order=TRUE,cex.text=0.7,
cex.legend=1,asb=TRUE,rotate_label=TRUE,
out_krona="for_krona.txt",text2krona=NULL)

Arguments

refpkg_path	The path of the reference package directory
type	The type of summary to perform with "summary", "taxonomy", "info", "tree", "pie" or "krona" available
rank_tree	The desired rank for tree coloring
rank_pie	The ranks to be plot for the taxonomy pie chart
scale_pie	Wether or not to take into account the number of sequences available within the reference package for the pie chart
alpha_order	Wether or not the color should follow taxa alpahabetic order when type set to "tree"
cex.text	The tip labels cex parameter when type is set to "tree" and the text cex parameter when type is set to "pie"
cex.legend	The size of the legend when type set to "tree"
asb	Add a scale bar on the tree
rotate_label	Rotates the pie slice labels
out_krona	The name of the output file when type is set to "krona".
text2krona	The full path to the krona "ImportText.pl" script when KronaTools is installed and you wish to directly produce the html krona file.

Value

A summary print on screen when type set to "summary". A data frame when type set to "taxonomy" or "info". A file written to the disk when type is set to "krona". A plot otherwise.

Author(s)

pierre lefeuvre

References

https://github.com/marbl/Krona/wiki/KronaTools http://fhcrc.github.io/taxtastic/

Examples

refpkg_path <- paste(find.package("BoSSA"),"/extdata/example.refpkg",sep="")

### summary
refpkg(refpkg_path)

### taxonomy
taxonomy <- refpkg(refpkg_path,type="taxonomy")
head(taxonomy)

### info
refpkg(refpkg_path,type="info")

### tree
refpkg(refpkg_path,type="tree",rank_tree="order",cex.text=0.5)

### pie
refpkg(refpkg_path,type="pie",rank_pie=c("class","order","family"),cex.text=0.6)

### krona
# it will produce a flat text file
# this file can be use as input for the the "ImportText.pl" krona script
# see https://github.com/marbl/Krona/wiki/KronaTools for more details on krona
## Not run: 
refpkg(refpkg_path,type="krona",out_krona="for_krona.txt")

## End(Not run)

BoSSA documentation built on Oct. 23, 2020, 7:55 p.m.