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KrishnaswamyLab / MAGIC

MAGIC (Markov Affinity-based Graph Imputation of Cells), is a method for imputing missing values restoring structure of large biological datasets.
GNU General Public License v2.0
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Stuck at "Calculating PCA..." #118

Closed BoyuLyu closed 6 years ago

BoyuLyu commented 6 years ago

While running MAGIC, it is stuck after printing "Calculating PCA". Besides, I couldn't find the code related to this part. The dataset I used was very small. The code I used: output <- magic(t(data), t=6, n,jobs=20)

BoyuLyu commented 6 years ago

Is there anyway I could install the previous version? That version runs well on my computer.

scottgigante commented 6 years ago

@HHHit we wrote the new version in order to greatly expand the computational capacity of MAGIC - ordinarily, the running speed of the new version is orders of magnitude faster than the old version.

If you could provide the rest of your code, I can debug it for you. The first thing I notice is that you have a comma instead of a period in n.jobs - I'm not sure if this is just a typo in the issue or actually in your code, though.

To see if this is an issue with the installation, could you please run the following in R:

library(Rmagic)
data(magic_testdata)
# Run MAGIC
data_magic <- magic(magic_testdata, npca=ncol(magic_testdata)-1, genes=c("VIM", "CDH1", "ZEB1"))

It should complete in under 30 seconds. If that doesn't work, please run the following from a terminal

pip uninstall numpy scipy scikit-learn magic
pip install --user --upgrade numpy scipy scikit-learn git+git://github.com/KrishnaswamyLab/MAGIC.git#subdirectory=python

and then try the R commands again. Please paste all of the code you run and all of the output so I can debug. Thanks, and sorry for the inconvenience!

scottgigante commented 6 years ago

I'm closing this issue due to lack of activity. Please feel free to reopen it if the issue persists.