I have a long standing unresolved question about the difference between heatmap.2 and pheatmap.
In general, we could see the clusters produced by pheatmap exhibit a more obvious color pattern (the genes with the similar colors in each row will cluster together first) rather than heatmap.2 (the genes with the similar colors are distributed).
Does it mean pheatmap outperform heatmap.2 in terms of gene expression profile cluster analysis?
Sometimes, even the clusters of samples look different.
Does anyone know if heatmap.2 usually generate a less clear pattern for the gene expression profiles, why should we use it for the analysis?