Tag density plot form chip or atac seq data I m quoting this  paper , figure B where they write 

"B) Violin plots for the normalized ATAC-seq tag density for all peaks within the indicated OC/CO groups at the indicated time points. Data were converted to a Z score based on the row-wise SD for each peak. ∗p &lt; 0.01 Mann-Whitney U test." 

My question is where is this tag density information coming from.

So far for chipseq data what I have done is


Aligned the data
Then all required data processing post alignment 
Generated bed and bigwig files of respective samples required for comparison
Made tag-directory using homer.
Then peak-calling using homer,annotated peak using homer.


Now so far I am not able to figure out where is this tag-density information is .

Any help or suggestion would be really appreciated.
You can use Homer to retrieve tag densities, quoting from their manual:


  Calculating ChIP-Seq Tag Densities across different experiments
  
  annotatePeaks.pl is [a] useful program for cross-referencing data from
  multiple experiments.  In order to count the number of tags from
  different sequencing experiments, you must first create tag
  directories for each of these experiments.  Once created, tag counts
  from these directories in the vicinity of your peaks can be added by
  specifying "-d   ...".  You can
  specify as many tag directories as you like.  Tag totals for each
  directory will be placed in new columns starting on column 18.  For
  example:
  
  annotatePeaks.pl pu1peaks.txt mm8 -size 400 -d Macrophage-PU.1/
  Bcell-PU.1/ > output.txt