####---- Differential Expression Signatures Heatmaps  ----####

plot_height = 500
plot_width = 500
colours = default_three_tone_heatmap_colours
sample_names = default_sample_labels
distance_method = "spearman"
clustering_method = "average"
reorder_function = "average"
cluster_x = FALSE
cluster_y = TRUE

for (signature in 1:nrow(signature_summary))
{
signature_genes = read.table(file=paste("<*path*>data/statistical_analysis/differential_expression_signature/gene_symbols/signature_",signature,"_symbols.txt<*/path*>",sep=""), header=FALSE,row.names = 1, sep='\t', quote='',check.names = TRUE)
signature_ne_matrix = Mde_annotated[row.names(signature_genes),samples]
signature_ne_matrix_scaled = data.frame(t(scale(t(signature_ne_matrix))))
rownames(signature_ne_matrix_scaled) = rownames(signature_ne_matrix)
signature_ne_matrix_scaled = na.omit(signature_ne_matrix_scaled)
signature_ne_matrix_scaled = signature_ne_matrix_scaled[is.finite(rowSums(signature_ne_matrix_scaled)), ]

ggp = make_significant_genes_heatmap(signature_ne_matrix_scaled,colours,sample_names,cluster_x,cluster_y,distance_method,clustering_method,reorder_function, sample_groupings, default_samples_colours)
save_plot(ggp,plot_height,plot_width,paste("<*path*>plots/differential_expression_signature/signature_heatmaps/signature_",signature,"_heatmap.png<*/path*>",sep=""))

}

