how can we create heat map for only upregulated gene list for FPKM treated vs control?
I am getting two solid color for treated and control resp not gradient color
what is the criteria for upregulation? If you are using fc/lfc, use a cut off to filter the data frame for upregulated data. Then use one of the heatmap plotting libraries (heatmap2 from gplots, complexheatmap, pheatmap, heatmap3 etc).
You need to filter your data.
There is not mention to the method you got your data, but you can use R, excel and many other programs to filter