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Add Drosophila data.

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This commit is contained in:
Neil Lawrence 2014-05-14 11:25:07 +01:00
parent 9171909724
commit 7293f4ca52
15 changed files with 48 additions and 9486 deletions
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34
GPy/util/datasets.py
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@ -391,6 +391,40 @@ def fruitfly_tomancak(data_set='fruitfly_tomancak', gene_number=None):
X = np.vstack((xtime.flatten(), xrepeat.flatten())).T
return data_details_return({'X': X, 'Y': Y, 'gene_number' : gene_number}, data_set)
def drosophila_protein(data_set='drosophila_protein'):
if not data_available(data_set):
download_data(data_set)
from pandas import read_csv
dirpath = os.path.join(data_path, data_set)
filename = os.path.join(dirpath, 'becker_et_al.csv')
Y = read_csv(filename, header=0)
return data_details_return({'Y': Y}, data_set)
def drosophila_knirps(data_set='drosophila_protein'):
if not data_available(data_set):
download_data(data_set)
from pandas import read_csv
dirpath = os.path.join(data_path, data_set)
filename = os.path.join(dirpath, 'becker_et_al.csv')
# in the csv file we have facts_kni and ext_kni. We treat facts_kni as protein and ext_kni as mRNA
df = read_csv(filename, header=0)
t = df['t'][:,None]
x = df['x'][:,None]
g = df['expression1'][:,None]
p = df['expression2'][:,None]
leng = x.shape[0]
T = np.vstack([t,t])
S = np.vstack([x,x])
inx = np.zeros(leng*2)[:,None]
inx[leng*2/2:leng*2]=1
X = np.hstack([T,S,inx])
Y = np.vstack([g,p])
return data_details_return({'Y': Y, 'X': X}, data_set)
# This will be for downloading google trends data.
def google_trends(query_terms=['big data', 'machine learning', 'data science'], data_set='google_trends'):
"""Data downloaded from Google trends for given query terms. Warning, if you use this function multiple times in a row you get blocked due to terms of service violations."""