In hsiujho/BacteriaIden:

require(BacteriaIden)
knitr::opts_chunk$set(echo = TRUE)

data("iris")

y0=iris[,-5]
y1=matrix(colnames(y0),ncol=1)
rownames(y1)=paste0("char",1:4)
colnames(y1)="Character"
colnames(y0)=rownames(y1)
y2=data.frame(Speices=iris[,5],A=0,B=1,stringsAsFactors = T)

iris_phylo=phyloseq(
otu_table(y0,taxa_are_rows = F)
,tax_table(y1)
,sample_data(y2)
)

p1=myord(phylo=iris_phylo,gv.name="Speices",plot.ellipse=T,plot.spider=T)

win.graph()
p1+scale_color_manual(breaks = c("setosa", "versicolor", "virginica")
                      ,values=c("red", "blue","black"),name="Speices")+ggtitle("IRIS")+xlab("xlab")+theme_bw()

hsiujho/BacteriaIden documentation built on May 17, 2019, 5:55 p.m.