Set scale for APA plots

[Bharath S]

Hello,
I would like to know if there was some way to set the same intensity scale to compare two HiC datasets while creating APA plots?

Thank You for your time

[Suhas Rao]

Hi Bharath,

Note that the max color scale is already set to 5 * the average of the values the upper right corner (as described in section VI.d. of Rao and Huntley et al, Cell 2014) so that it is comparable between data sets despite any differences in sequencing depth. 

If you want to set your own color scale, you can pass the -u flag to the apa command and the data underlying the APA matrix will be dumped as well so that you can plot it yourself using a custom color scale.

Best,

Suhas

[Bharath S]

Thank You very much.