How to have frequency displayed on the Y axis in weblogo

Question

[Aishwarya Kulkarni]

I am using weblogo http://weblogo.berkeley.edu/logo.cgi to try and generate weblogos with frequency (upto 100) displayed on Y axis, I assumed checking the box for frequency plot would do it but I get no display on the Y axis How can it be changed to display frequency on Y axis ?

[Robert W Link]

did you try checking the "frequency plot" box on the options?

Answer 1

[Alex Reynolds]

Within weblogo, add the --units probability argument (or select probability from the Units pull-down menu from the web interface) and edit the figure with Illustrator (PDF/SVG) or Inkscape (SVG) to modify the y-axis, changing fractional probability ([0,1]) to a percentage ([0,100]) by multiplying fractional probability by 100. Refer to the manual for more detail.