We used the Profile function in DANPOS version 2.2.3 to compare the 4 epigenetic profiles between putative identity genes and control genes around the promoter region (-3kb to 10kb of TSS):

python danpos.py profile wig --genefile_paths putative_identity_genes.txt,putative_negative_identity_genes.txt --genefile_aliases positive,negative --heatmap 1 --name outdir --genomic_sites TSS --flank_up 3000 --flank_dn 10000

Heatmaps were created using HEATMAP.R.

Scatter plot is created based on CIG score and gene ranking, very known cell identity genes for the corresponding cell type are marked with red color.