Entering edit mode
22 months ago
Ric
▴
440
Hi,
I found the below Upset plot code from Wayne here. The Orthogroups.GeneCount.tsv
can be found here
import pandas as pd
dic={'group':[],'sp1':[],'sp2':[],'sp3':[],'sp4':[],'sp5':[],'sp6':[],'total':[]}
with open ("Orthogroups.GeneCount.tsv","r") as f:
f.readline()
line = f.readline()
while line:
parts = line.strip().split("\t")
dic['group'].append(parts[0])
dic['sp1'].append(parts[1])
dic['sp2'].append(parts[2])
dic['sp3'].append(parts[3])
dic['sp4'].append(parts[4])
dic['sp5'].append(parts[5])
dic['sp6'].append(parts[6])
dic['total'].append(parts[7])
line = f.readline()
df = pd.DataFrame(data=dic).set_index("group")
cols = df.columns[df.dtypes.eq('object')] # based on https://stackoverflow.com/a/36814203/8508004
df[cols] = df[cols].apply(pd.to_numeric, errors='coerce') # based on https://stackoverflow.com/a/36814203/8508004
group_dict = {}
for index, row in df.iterrows():
for sp, count in row.items():
if sp != "total" and count != 0:
group_dict.setdefault(index, []).append(sp)
group_dict
# import pyupset as pyu
from upsetplot import UpSet
from upsetplot import from_memberships
x = from_memberships(group_dict.values()).sort_values(ascending=False)
UpSet(x, subset_size='count', show_counts=True).plot()
from matplotlib import pyplot as plt
plt.title("UpSet with catplots, for orientation='horizontal'")
plt.show()
How is it possible to prevent the labels are overlapping?
I appreciate any help you can provide.
Best wishes,
It does not work for me. Everything gets smaller except the numbers.
. What did I miss?
P.S. Is it possible to rotate the values to portrait?