library(prabclus)
library(Matrix)
library(Rtsne)
library(ggplot2)
Loading required package: MASS Loading required package: mclust Package 'mclust' version 5.4.3 Type 'citation("mclust")' for citing this R package in publications.
load(file = '../../run_methods/Scasat/Scasat_cusanovich2018subset.RData')
set.seed(2019)
my.dist <- as.dist(getJaccardDist(cdBinary))
my.tree <- hclust(my.dist, method = "ward.D2")
#library(dynamicTreeCut)
#my.clusters <- unname(cutreeDynamic(my.tree, distM=as.matrix(my.dist), verbose=0))
nClusters = length(levels(as.factor(metadata$label)))
df_pre = data.frame('Scasat'=cutree(my.tree,nClusters))
df_pre$ord = 1:nrow(df_pre)
df_pre = df_pre[as.character(rownames(metadata)),]
df_out = data.frame('Scasat'=df_pre[,'Scasat'])
rownames(df_out) = rownames(df_pre)
write.table(df_out,file="clusteringSolution.tsv", quote=FALSE, sep='\t', col.names = NA)