The same number of significantly expanded and contracted families

[Justin Choi]

Hello,

I really like this fantastic program to draw Cafe output files. When I used it with my data, the numbers of significantly expanded and contracted families are the same while the example data showed the different numbers. Could you check if this is correct?

Thanks,
Justin
cafe_result.txt
summary.pdf

[jinhaoding]

@methylome
Hi，I have the same problem.
Can you tell me if you've solved it.

Thanks,
Ding

[Justin Choi]

@dingcaojin
I haven't solved it.

Thanks,
Justin

[YuzhouGong]

Hi guys,
I have encountered a similiar problem, when I used the example data without the --count_all_expansions option, the result showed same numbers in expanded and contracted gene families, like this:

But when I added --count_all_expansions, the result seemed to be correct, like this:

As for my own data, because I'm using CAFE5, the result generated by cafe_fig is not correct when skipping --count_all_expansions, all nodes show +0 -0 pattern on the phylogenetic tree.
Seems like cafe_fig must rely on option count_all_expansions to draw the right number on trees.