In order to make some of the above easier, we created the shinyHeatmaply package (available on CRAN) which offers a GUI to help guide the researcher with the heatmap construction, with the functionality to export the heatmap as an html file and summaries parameter specifications to reproduce the heatmap with heatmaply. For a more detailed step-by-step demonstration of using heatmaply on biological datasets, you should explore the heatmaplyExamples package (https://github.com/talgalili//heatmaplyExamples).