search

mkanai / fujiplot

:mount_fuji: Fuji plot—a circos representation of multiple GWAS results— :mount_fuji:
https://www.nature.com/articles/s41588-018-0047-6
GNU General Public License v3.0
73 stars 19 forks source link

Problem with the output figure.... #5

Closed MuBulut closed 4 years ago

MuBulut commented 4 years ago

Hi, I wanted to run now the script with my dataset, and this type of error occurs.....

image

The output seems empty, are there any limitations with the numbers of traits, since I have 920 traits...

My Trait list looks like this:

[I have in total two categories ..._BASE and .....GROUP]

My input file look like this:

[The trait is basically a mass feature of an unknown compound and the Gene is the same as the Locus ID since I do not have information of the gene in those regions]

EDIT: Found the problem most likely....

image

Is there a way to increase the highlighted data points?

EDIT:

image

Changed it in the housekeeping.config file accordingly [=2.991.000 to be sure], but still indicates that I need to change the threshold from 25.000 up to atleast 29.910.....

Thanks. Mustafa

mkanai commented 4 years ago

Hi, thanks for reaching out and apologies for the delay in getting back to you. I'm not sure why housekeeping.conf doesn't take effect... Would you mind testing whether the script works with a smaller input file?

I wonder, even when housekeeping.conf works, the output might become too dense with 29910 points, though...

MuBulut commented 4 years ago

Ok, now I got an output by reducing the files to 24.949 points. You are right it is way to dense..... I think I will perform further filtering before performing the script. At least now the script works for my data. Thanks

mkanai commented 4 years ago

Great! Please let me know if you have any other questions.

Thanks, Masa