I hereby claim:
- I am gokceneraslan on github.
- I am gokcen (https://keybase.io/gokcen) on keybase.
- I have a public key whose fingerprint is 8755 72CC F7D6 DF05 0C63 8DCF 47D6 92B1 11C3 8A5F
To claim this, I am signing this object:
diff --git a/prody/dynamics/plotting.py b/prody/dynamics/plotting.py | |
index 994f5f2..c5d54cf 100644 | |
--- a/prody/dynamics/plotting.py | |
+++ b/prody/dynamics/plotting.py | |
@@ -511,7 +511,7 @@ def showCrossProjection(ensemble, mode_x, mode_y, scale=None, *args, **kwargs): | |
return show | |
-def showOverlapTable(rows, cols, *args, **kwargs): | |
+def showOverlapTable(rows, cols, **kwargs): |
#!/usr/bin/env python | |
import urllib2 as ul | |
from lxml import etree | |
def parse_votes(url): | |
doc = ul.urlopen(url).read() | |
tree = etree.HTML(doc) | |
res = {} |
# labels is a NxL data.frame where N=number of observations being clustered and | |
# L = number of clustering results (number of vertical lines) | |
plot.label.distribution <- function(labels, | |
groupColumn, | |
alphaLines = 1/10, | |
useSplines = T, | |
showPoints = T, | |
scale='uniminmax', ...) { |
bin.signal <- function(data, bin.width) { | |
if (is.matrix(data)) data <- list(data) | |
lapply(data, function(d) { | |
window.size <- ncol(d) | |
res <- t(apply(d, 1, function(row) { | |
sapply(seq(1, window.size, bin.width), function(s) sum(row[s:(s+bin.width-1)])) | |
})) | |
colnames(res) <- paste0('bin', seq_len(ncol(res))) | |
res |
I hereby claim:
To claim this, I am signing this object:
library(FNN) | |
library(parallel) | |
# cnt: cell x gene matrix (can be raw count or library size normalized, but not log transformed) | |
impute <- function(cnt, k=30, cores=6, pca.dim=100) { | |
print(paste0('Starting imputation with ', nrow(cnt), ' cells and ', ncol(cnt), ' genes...')) | |
print('Performing PCA...') | |
pca <- prcomp(log(cnt+1), center = T, rank.=pca.dim)$x | |
import os | |
import numpy as np | |
import pandas as pd | |
import plotnine as p9 | |
from tqdm import tqdm | |
import torch | |
from torch.autograd import Variable | |
from torch.utils.data import TensorDataset, DataLoader |
import numpy as np | |
import pandas as pd | |
import plotnine as p9 | |
import torch | |
from torch.autograd import Variable | |
from torch.utils.data import TensorDataset, DataLoader, Dataset | |
np.random.seed(555) | |
torch.manual_seed(555) |