search

SystemsGenetics / KINC

Knowledge Independent Network Construction
MIT License
11 stars 4 forks source link

Kinc 3D viewer requires that the first column of the amx be labled "Sample" #158

Open JohnHadish opened 4 years ago

JohnHadish commented 4 years ago

This is not the case for the rest of KINC.

spficklin commented 4 years ago

@JohnHadish there is a --sample_col argument to the 3D viewer that lets you set the name of the sample column. But your question makes me realize there isn't good help instructions for the tool. I'll fix it.

spficklin commented 4 years ago

PR resolves this issue.

JohnHadish commented 4 years ago

Still requires user to set a column name, which is inconsistent with the rest of KINC. I am of the opinion that if the user is able to get to this point without renaming their data/ setting a --sample-column arguement, that they should not be required to do so during the inal step

spficklin commented 4 years ago

I think KINC itself needs this argument. In the cond-test analytic, KINC looks for a column named 'Sample' in the amx file and if it can't find it, then it defaults to using the first column regardless of what's in it. This is not mentioned in the documentation for the argument and may cause a problem for folks who's amx file doesn't follow either of those expectations.