Hi, you may want to take a look at my answer here, where I have done specifically this: Heatmap based with FPKM values

You will have to get your data in this format:

      Sample1 Sample2 Sample3 Sample4 ...
Gene1 45      453       2       4
Gene2 45       43     444      53
Gene3 40        3      23     232
Gene4 50       56      43     224
...

Hello, I wrote a python module named Papillon for this purpose. Python normally is easier to learn than R. You can find Papillon here. There is a tutorial, you can install it with pip or conda, and make a heatmap is very easy:

import papillon as pp

MyExp=pp.read_db("My Experiment")                # "My Experiment" is the folder name of your data

MyExp.get_gene()             # you can select gene/isoform o specific gene name (see the tutorial)

MyExp.heatmap(z_score=True)

Best Regards Dom