DiffLogo can give totally wrong logo plots if matrix rownames are in the wrong order

[jayoung]

hi there,

I found out (the hard way) that DiffLogo can give logos that at first glance look OK, but in fact are showing the wrong letters entirely. It happens when the rows of the input frequency matrix are not ordered in the same way as the chars field of the Alphabet being used.

Reproducible example code is here: https://github.com/jayoung/janet_stuff_to_share/blob/main/DiffLogo/DiffLogo_tests.md

It would be really great if DiffLogo::seqLogo and diffLogoFromPwm were able to check that the matrix and alphabet are compatible, to avoid producing wrong logos.

thanks!

Janet

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Janet Young
Fred Hutch Cancer Center