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Devel #231

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merged 8 commits into from
Nov 19, 2021
Merged

Devel #231

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5373c00
Merge pull request #225 from netZoo/master
marouenbg Oct 29, 2021
5515895
fix alpaca single gene community
marouenbg Oct 29, 2021
10f4867
Merge pull request #226 from marouenbg/fix-alpaca-error
marouenbg Oct 29, 2021
d3c3b19
Merge pull request #228 from netZoo/master
marouenbg Nov 14, 2021
d2d0388
os specific file path
marouenbg Nov 18, 2021
1df6423
add os as library in python
marouenbg Nov 18, 2021
5703353
removed path
marouenbg Nov 18, 2021
c264ea2
Merge pull request #230 from marouenbg/fix-filepath
marouenbg Nov 18, 2021
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13 changes: 8 additions & 5 deletions R/ALPACA.R
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Original file line number Diff line number Diff line change
Expand Up @@ -70,19 +70,22 @@ alpaca <- function(net.table,file.stem,verbose=FALSE)
louv.Bscores <- NULL
for (i in seq_len(max(louv.memb)))
{
print(i)
this.comm <- names(louv.memb)[louv.memb==i]
this.tfs <- this.comm[grep("_A$",this.comm)]
this.genes <- this.comm[grep("_B$",this.comm)]
if (length(this.tfs)>=1){
if (length(this.tfs)>1){
tf.sums <- apply(dwbm[this.tfs,this.genes],1,sum)
gene.sums <- apply(dwbm[this.tfs,this.genes],2,sum)
if (length(this.genes)==1){
gene.sums <- sum(dwbm[this.tfs,this.genes])
tf.sums <- dwbm[this.tfs,this.genes]
}else if (length(this.genes)>1){
tf.sums <- apply(dwbm[this.tfs,this.genes],1,sum)
gene.sums <- apply(dwbm[this.tfs,this.genes],2,sum)
}
} else if (length(this.tfs)==1) {
tf.sums <- sum(dwbm[this.tfs,this.genes])
gene.sums <- dwbm[this.tfs,this.genes]
} else if (length(this.genes)==1){
gene.sums <- sum(dwbm[this.tfs,this.genes])
tf.sums <- dwbm[this.tfs,this.genes]
}
this.denom <- sum(dwbm[this.tfs,this.genes])
louv.Ascores <- c(louv.Ascores,tf.sums/this.denom)
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7 changes: 4 additions & 3 deletions inst/extdata/panda.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,7 @@
import pandas as pd
from scipy.stats import zscore
import numpy as np
import os

# this scirpt is derived from https://github.com/netZoo/netZooPy/blob/master/netZooPy/panda/panda.py
# and https://github.com/netZoo/netZooPy/blob/master/netZooPy/panda/timer.py
Expand Down Expand Up @@ -91,9 +92,9 @@ def __init__(self, expression_file, motif_file, ppi_file, computing='cpu',precis
if save_tmp:
with Timer('Saving expression matrix and normalized networks ...'):
if self.expression_data is not None:
np.save('/tmp/expression.npy', self.expression_data.values)
np.save('/tmp/motif.normalized.npy', self.motif_matrix)
np.save('/tmp/ppi.normalized.npy', self.ppi_matrix)
np.save('expression.npy', self.expression_data.values)
np.save('motif.normalized.npy', self.motif_matrix)
np.save('ppi.normalized.npy', self.ppi_matrix)

# delete expression data
del self.expression_data
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