how to normalize two files and compare them in heatmap

[jiangshan529]

Hi, I use bamcoverage RPKM to normalize individual samples. Now I want to compare two different chip-seq samples by visualizing them in heatmap, is RPKM normalization to each individual sample enough? Do I need to do other things to normalize the two? I see Bamcompare, but it generates a single log2 bigwig file, but I want to plot two heatmaps(each sample with a heatmap). Thanks!