envis.NB: Visualize The Negative Binomial Model OF A Given Taxon OR...

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

Description

This function plot the negative binomial model for a given otuID or taxon

Usage

envis.NB(NB.model="", tax.meta,  taxon="",
         x="", num.col=NULL, group=NULL, group.order=NULL,
         xlab=NULL, ylab=NULL, fill=NULL, facet=NULL,
         file=NULL, ext=NULL, width=8, height=8)

Arguments

NB.model	the negative binomial model. Can be obtained by using assist.NB
tax.meta	the combined taxon/otuID and metadata. Can be obtained by using assist.NB
taxon	the taxon or otuID. Can be obtained by using assist.NB
x	a metadata variable name for x axis.
num.col	optional. A metadata numerical variable that will be used as predictor.
group	optional. A metadata factor variable that will be used as predictor.
group.order	optional. The desired order for the group.
xlab	optional. X axis label.
ylab	optional. Y axis label.
fill	optional. Color for fill different categories.
facet	optional. Metadata category variables as faceting variables.
file	optional. Filename that the plot to be saved to.
ext	optional. Filename extension, type of image to be saved.
width	an integer. Filter OTU table by counts.
height	an integer. Filter OTU table by counts.

Value

This function plot predicted taxon/otuID under the impact of metadata variables.

Author(s)

Wen Chen

Examples

data(ITS1, meta)
# filter otu table
its1 <- filter.OTU(data=list(ITS1=ITS1), percent=0.01)[[1]]
m <- meta[, c(2,3,5,7)]
## Not run: 
# test the model
nb <- assist.NB(its1, meta=m, rank="g", 
                anov.fac="Harvestmethod",
                taxon=rownames(its1)[1])
NB.model<-nb[[1]]
tax.meta<-nb[[2]]
taxon<-nb[[3]]
envis.NB(NB.model=NB.model, tax.meta=tax.meta,  taxon=taxon,
                x="Ergosterol_ppm", num.col="Ergosterol_ppm",
                group="Crop", group.order=NULL,
                xlab="Ergosterol (ppm)", ylab=NULL,
                fill="Harvestmethod", facet=c("City","Crop"))

## End(Not run)

Example output

Loading required package: vegan
Loading required package: permute
Loading required package: lattice
This is vegan 2.5-4
Loading required package: ggplot2
[1] "26 otus in ITS1 met the filter requirment."
[1] "A total of  0  columns are removed:  "
[1] "columns in exclude list: "
[1] "column# with missing data: "
[1] "columns# with one level: "
[1] "column# that are not numeric or factor: "
Warning message:
In assist.NB(its1, meta = m, rank = "g", anov.fac = "Harvestmethod",  :
  Test an otuID, will ignore the ranks
Warning message:
In envis.NB(NB.model = NB.model, tax.meta = tax.meta, taxon = taxon,  :
  Divide plots to 2 columns

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