If there are NaN in the output from computeMatrix, the generated heatmap is not sorted and a warning message stating Mean of empty slice will show up.

To overcome this, those null values need to be replaced using 0 in the computeMatrix step by --missingDataAsZero tag.

computeMatrix scale-regions -S xxx.bw -R xxx.bed --missingDataAsZero -m xxx -b xxx -a xxx --numberOfProcessors xx -o xxx.gz

plotHeatmap -m xxx.gz -out xxx.png

Source:
https://groups.google.com/g/deeptools/c/B55e0kT_0Ec?pli=1
https://github.com/deeptools/deepTools/issues/490