Nothing
# Julia Bischof
# 12-08-2015
#library(vegan)
#library(proxy)
geneUsage.distance<-function(geneUsage.tab=NULL, names=NULL, method=c("bc","jaccard", "cosine"), cutoff=0){
if(length(geneUsage.tab)==0){
stop("--> gene usage table is missing")
}
if(length(method)!=1){
stop("--> Please choose one method")
}
if(method=="bc"){
dist<-"bray"
}else if(method=="jaccard" && length(cutoff)==1){
temp<-geneUsage.tab
geneUsage.tab<-matrix(0, ncol=ncol(temp), nrow=nrow(temp))
for(i in 1:nrow(geneUsage.tab)){
geneUsage.tab[i,which(temp[i,]>cutoff)]<-1
}
dist<-"jaccard"
}
if(method=="cosine"){
tab<-as.matrix(dist(geneUsage.tab, method="cosine"))
}else{
tab<-as.matrix(vegdist(geneUsage.tab, method = dist))
}
colnames(tab)<-if(length(names)>0){names}else{paste("Sample",1:nrow(geneUsage.tab),sep="")}
rownames(tab)<-if(length(names)>0){names}else{paste("Sample",1:nrow(geneUsage.tab),sep="")}
return(tab)
}
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.