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#Author: Gaetan Benoit
#Contact: gaetan.benoit@inria.fr
args <- commandArgs(trailingOnly = TRUE)
distanceMatrixFilename = args[1]
distance_name = basename(distanceMatrixFilename)
distance_name = unlist(strsplit(distance_name, "[.]"))[1]
distance_name = gsub("mat_", "", distance_name)
distanceMatrix = as.matrix(read.table(file=distanceMatrixFilename, sep=";", header=TRUE, row.names=1))
distanceMatrix[lower.tri(distanceMatrix)] <- t(distanceMatrix)[lower.tri(distanceMatrix)] #symmetrize matrix
width = as.numeric(args[3])
height = as.numeric(args[4])
format = args[5]
if(format == "png"){
png(file=paste0(args[2], ".png"), width=width, height=height, units="in",res=72)
} else{
pdf(file=paste0(args[2], ".pdf"), width=width, height=height)
}
use_metadata = F
if(length(args) == 7){
suppressPackageStartupMessages(library(dendextend))
use_metadata = T
metadata_table = as.matrix(read.table(file=args[6], sep=";", header=TRUE, row.names=1))
metadata_variable = args[7]
#print(metadata_table)
variables = metadata_table[,metadata_variable]
#print(variables)
meatadata_index = list()
dataset_ids = rownames(metadata_table)
for(i in 1:length(dataset_ids)){
dataset_id = dataset_ids[i]
#print(dataset_id)
#print(variables[[i]])
meatadata_index[[dataset_id]] = variables[[i]]
print(paste0(dataset_id, " ", variables[[i]]))
#print(meatadata_index[[dataset_id]])
}
colors = c()
dataset_ids = rownames(distanceMatrix)
for(i in 1:dim(distanceMatrix)[1]){
dataset_id = dataset_ids[i]
colors = c(colors, meatadata_index[[dataset_id]])
}
colors_numeric_temp = c()
colors_numeric = as.numeric(as.factor(colors))
for(i in 1:length(colors_numeric)){
colors_numeric_temp = c(colors_numeric_temp, colors_numeric[i]+1)
}
colors_numeric = colors_numeric_temp
#print(colors)
}
distanceMatrix = distanceMatrix*100
#inv_cr3 = matrix(100, ncol=dim(cr3)[1], nrow=dim(cr3)[1]) - cr3
Commet_distance = as.dist(distanceMatrix)
hc = hclust(Commet_distance, method="average")
dendo_cr3 = as.dendrogram(hc)
if(use_metadata){
colors_numeric_hc = colors_numeric[hc$order]
dendo_cr3 %>% set("labels_col", colors_numeric_hc) %>% set("branches_k_color", colors_numeric_hc) %>% # change color
plot(main=paste0("Simka hierarchical clustering\n", distance_name), cex = 0.3, xlab="", sub="")
legend("topright", title=metadata_variable, legend=unique(colors), col=unique(colors_numeric), pch=16)
} else{
plot(dendo_cr3, main=paste0("Simka hierarchical clustering\n", distance_name), cex = 0.3, xlab="", sub="")
}
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