damienarnol / svca Goto Github PK
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License: Apache License 2.0
Why do you use the whitespace as the sep in expressions.txt but use the comma in positions.txt?
Is that some joke to you?
Have fun developing no-one-want-to-use methods!
If you check this two lines of the plotting script:
svca/SVCA/svca/plot_scripts/visu_signatures_functions.R
Lines 26 to 27 in e2fa3d0
it seems you are looking for filenames in the results folder, which contains both words "effect" and "interactions".
But if I check the directory where you have the results, I only see file names that contains
intrinsic_effects or
env_effects or
local_effects.
maybe it is a typo interaction --> intrinsic?
I managed to submit the jobs by run_all_cluster.py, but got an error:
from the log file:
ag252714@cluster:~/svca/SVCA/svca/run_cluster[659]$ vim tmp_log
Traceback (most recent call last):
File "../run/run_indiv.py", line 59, in
run(data_dir, protein_index, output_dir, normalisation)
File "../run/run_indiv.py", line 36, in run
model = Model1(phenotype, X, norm=normalisation, oos_predictions=0., cov_terms=cterms, kin_from=kin_from, cv_ix=0)
File "/home/ag252714/.local/lib/python2.7/site-packages/svca/models/model1.py", line 49, in init
self.init_model(cov_terms)
File "/home/ag252714/.local/lib/python2.7/site-packages/svca/models/model_base.py", line 84, in init_model
self.build_cov(cov_terms)
File "/home/ag252714/.local/lib/python2.7/site-packages/svca/models/model1.py", line 81, in build_cov
self.covar = apply(SumCov, self.covar_terms.values())
File "/home/ag252714/.local/lib/python2.7/site-packages/limix/core/covar/combinators.py", line 22, in init
self.addCovariance(covar)
File "/home/ag252714/.local/lib/python2.7/site-packages/limix/core/covar/acombinators.py", line 22, in addCovariance
assert covar.dim==self.dim, 'Dimension mismatch.'
File "/home/ag252714/.local/lib/python2.7/site-packages/limix/core/covar/zkz.py", line 46, in dim
return self.K().shape[0]
File "/home/ag252714/.local/lib/python2.7/site-packages/limix/hcache/_hcache.py", line 173, in method_wrapper
result = method(self, *args, **kwargs)
File "/home/ag252714/.local/lib/python2.7/site-packages/limix/core/covar/zkz.py", line 180, in K
K = self._K()
File "/home/ag252714/.local/lib/python2.7/site-packages/limix/hcache/_hcache.py", line 173, in method_wrapper
result = method(self, *args, **kwargs)
File "/home/ag252714/.local/lib/python2.7/site-packages/limix/core/covar/zkz.py", line 224, in _K
z = self.se.K()
File "/home/ag252714/.local/lib/python2.7/site-packages/limix/hcache/_hcache.py", line 173, in method_wrapper
result = method(self, args, **kwargs)
File "/home/ag252714/.local/lib/python2.7/site-packages/limix/core/covar/sqexp.py", line 194, in K
return self.scale * sp.exp(-self.E()/(2self.length))
File "/home/ag252714/.local/lib/python2.7/site-packages/limix/hcache/_hcache.py", line 173, in method_wrapper
result = method(self, *args, **kwargs)
File "/home/ag252714/.local/lib/python2.7/site-packages/limix/core/covar/sqexp.py", line 183, in E
rv = SS.distance.pdist(self.X,'euclidean')**2.
File "/usr/lib64/python2.7/site-packages/scipy/spatial/distance.py", line 1176, in pdist
dm = np.zeros((m * (m - 1) / 2,), dtype=np.double)
TypeError: 'float' object cannot be interpreted as an index
just some comments:
right now, setup is for personal computer and the example is supposed to run on the cluster. Consider making it coherent.
You could include a script for a subset of proteins/images that could be run on a local machine in a few minutes, so that the reviewer could try your script and then belive that the pipeline for the other images and proteins are also working.
I think if you have this script then you dont need to give instructions how to install your packages on a cluster. People can figure out themselves.
Anyway, the current installation instructions are not working on the cluster because of permission issues. As you said, conda environments would probably solve the issue, but then you might include a link how to do that.
The way it worked for me on the RWTH cluster by using pip
and the --user
option (credit for @Nic-Nic ):
git clone https://github.com/damienArnol/svca.git
cd svca/svca_limix
pip install --user ./
-- an issue could be that I could not pass the develop
argument for the setup.py script. But pip was able to install it anyway.cd ../SVCA
pip install --user ./
Hi there,
I have SVCA installed but I can't figure out how to execute the "call_run_indiv.sh" bash script from anaconda prompt on a windows machine?
Any help would be greatly appreciated!
Steve
I want to obtain the R^2 values of the prediction, and the function write_r2 is outputting Nan values.
When I looked at the predictions array they come out empty even with model.gp.predict(). I am unsure how I can obtain the predictions and thus the R^2 values.
I currently have svca installed, as well as my data (MIBI) formatted in the correct expression.txt and positions.txt folders. When I go to run the altered 'run_all_cluster.py' script I keep getting the error below:
workComputer:run_cluster id$ python run_all_cluster_fig6.py
Traceback (most recent call last):
File "run_all_cluster_fig6.py", line 1, in <module>
from svca.util_functions import cluster_utils, util_functions
File "/anaconda3/lib/python3.7/site-packages/svca-0.0.1-py3.7.egg/svca/util_functions/cluster_utils.py", line 6, in <module>
ModuleNotFoundError: No module named 'util_functions'
I'm running everything from terminal on a Mac, not sure if that matters.
Thanks!
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