I am trying to create heatmaps. I have used heatmap.2, pheatmap and clustvis. I have dataset of 2000 rows containing allele frquency of different SNPs in different populations. I cannot filter rows as I am visualizing relationship between different populations on the basis of allele frequencies. The problems with R packages is that they does not create good resolution heatmaps. And clustvis plots heatmaps on the basis of principal components not on the basis of actual allele freqiencies.
Can anyone please tell me how to great good resolution heatmaps of such large datasets?