파이썬 유용 함수 모음
추천글 : 【Python】 파이썬 목차, 【생물정보학】 생물정보학 분석 목차
1. 개요 [본문]
2. 기초 함수 [본문]
3. 파일 입출력 [본문]
4. 자료구조 [본문]
5. 이미지 처리 [본문]
6. 데이터 사이언스 [본문]
7. 딥러닝 함수 [본문]
8. 예외 처리 [본문]
9. 생물정보학 [본문]
a. GitHub (executable .py file)
c. 파이썬 앱 라이브러리
1. 개요 [목차]
⑴ 아래에서 정의한 함수는 다음과 같이 호출할 수 있음 : GitHub에서 python으로 .py 파일을 호출하는 방법
### Reference : https://changhsinlee.com/colab-import-python/
import requests
# Save datagenerators as file to colab working directory
# If you are using GitHub, make sure you get the "Raw" version of the code
url = 'https://github.com/JB243/nate9389/blob/main/Python/A_Collection_of_Useful_Functions_in_Python.py?raw=true'
r = requests.get(url)
# make sure your filename is the same as how you want to import
with open('A_Collection_of_Useful_Functions_in_Python.py', 'w') as f:
f.write(r.text)
# now we can import
from A_Collection_of_Useful_Functions_in_Python import SUM
### Warning
# Only SUM is implemented, but it seems to be implemented only at the beginning
SUM(2,6)
⑵ 아래에서 정의한 함수는 다음과 같이 사용할 수 있음 : 파이썬은 C언어처럼 함수를 정의 시 def를 사용
def SUM(a, b):
return a+b
SUM(1,2)
# 3
⑶ 파이썬 특징
① 파이썬은 여러 개의 값을 동시에 return할 수 있음
② back space \ 를 통해 줄바꿈을 하여 multi-line code를 짤 수 있음
③ 한 줄 문자열은 "~" 혹은 '~'로 나타내고, 여러 줄 문자열은 """~""" 혹은 '''~'''로 나타냄
④ adata.var_names=[i.upper() for i in list(adata.var_names)]
○ 의미 : adata.var_names에는 list(data.var_names)에 있는 각 i를 대문자로 한 것으로 저장
⑤ if issparse(counts.X):counts.X=counts.X.A
○ 의미 : counts.X가 sparse matrix이면 counts.X에 counts.X.A 값을 넣음
⑥ pd.DataFrame([(str(i),str(j)) for i in range(4) for j in range(i+1, 4)])
0 1
0 0 1
1 0 2
2 0 3
3 1 2
4 1 3
5 2 3
2. 기초 함수 [목차]
⑴ 타입 체크
type(x)
⑵ x초만큼 대기
time.sleep(x)
⑶ 배열 길이 및 차원
### length ###
len(x)
### dimensionality ###
x.shape # numpy.ndarray; cv2.imread
x.size # PIL.PngImagePlugin.PngImageFile; PIL.Image.open
⑷ 자연수 앞에 0을 채워서 총 다섯 자리가 되도록 하는 함수
n = 55
idx = str(n).zfill(5)
⑸ 주어진 문자열을 모두 소문자로 혹은 모두 대문자로
_str = "ABCdef"
_str.lower()
# 'abcdef'
_str.upper()
# 'ABCDEF'
⑹ 주어진 문자열에서 특정 문자열로 시작하는지 여부
a = "ABCD"
a.startswith('AB')
# TRUE
''' if a is not string object
a.str.startswith('AB')
# TRUE
'''
⑺ 주어진 문자열에서 특정 문자열로 끝나는지 여부
a = "ABCD"
a.endswith('CD')
# TRUE
⑻ 주어진 문자열(given_str)에서 특정 문자열(partial_str)을 포함하는지 여부
def is_contain(given_str, partial_str):
s = ''
for char in given_str:
s = s + char
if s.endswith(partial_str):
return True
return False
⑼ 주어진 문자열(str)에서 앞 몇 개의 문자를 제거한 뒤 반환하는 함수
def str_omit_forward(_str, n):
return _str[n:]
⑽ 주어진 문자열(str)에서 뒤 몇 개의 문자를 제거한 뒤 반환하는 함수
def str_omit_backward(_str, n):
return _str[:-n]
⑾ 주어진 원소(e)가 리스트(l)에 포함되는지 여부
def is_element_in_list(e, l):
for i in range(len(l)):
if e == l[i]:
return True
return False
⑿ 주어진 원소(e)가 리스트(l) 내 몇 번째 원소인지를 출력하는 함수
def where_element_in_list(e, l):
for i in range(len(l)):
if e == l[i]:
return i
return -1
⒀ 두 리스트의 교집합을 출력하는 함수
def is_element_in_list(e, l):
for i in range(len(l)):
if e == l[i]:
return True
return False
def my_intersection(l1, l2):
l = []
flag = 0
for i in range(len(l1)):
if is_element_in_list(l1[i], l2):
l[flag] = l1[i]
flag = flag + 1
return l
⒁ 날짜 표기 변환 함수 : 'Mar 02, 2018'을 20180301로 변환
def convert_date(_str):
def month_to_num(_str):
if _str == 'Jan':
return '01'
if _str == 'Feb':
return '02'
if _str == 'Mar':
return '03'
if _str == 'Apr':
return '04'
if _str == 'May':
return '05'
if _str == 'Jun':
return '06'
if _str == 'Jul':
return '07'
if _str == 'Aug':
return '08'
if _str == 'Sep':
return '09'
if _str == 'Oct':
return '10'
if _str == 'Nov':
return '11'
if _str == 'Dec':
return '12'
flag = 0
s1 = '' # Mar
s2 = '' # 01
s3 = '' # 2018
for char in _str:
## closing
if char == ' ' and flag == 0:
flag = 1
elif char == ',' and flag == 1:
flag = 2
elif char == ' ' and flag == 2:
flag = 3
## propagation
elif flag == 0:
s1 = s1 + char
elif flag == 1:
s2 = s2 + char
elif flag == 3:
s3 = s3 + char
return str(s3) + str(month_to_num(s1)) + str(s2)
⒂ 두 개의 리스트로 데이터프레임을 만드는 방법
import pandas as pd
v1 = []
v2 = []
...
df = pd.DataFrame(
{'Column1': v1,
'Column2': v2
})
⒃ 주어진 함수 MyFunc의 내용물 보기
import inspect
lines = inspect.getsource(MyFunc)
print(lines)
⒄ 변수 이름을 문자열(string)로 받고, 그 값을 동적으로 활용
def set_variable_from_string(variable_name, value):
globals()[variable_name] = value
def get_variable_value_from_string(variable_name):
return globals().get(variable_name, None)
# 변수 이름을 문자열로 설정
var_name = "sample_variable"
# 문자열을 사용하여 변수 생성
set_variable_from_string(var_name, 12345)
# 문자열을 사용하여 변수 값을 가져옴
value = get_variable_value_from_string(var_name)
print(f"{var_name} = {value}")
3. 파일 입출력 [목차]
⑴ csv 파일 읽기
import pandas as pd
x = pd.read_csv("FILE.csv", header=None, names= ['barcodes','tissue','row','col','imgrow','imgcol'])
⑵ 텍스트 파일 읽기
import csv
import sys
def read_txt(txt_dir):
l = []
f = open(txt_dir, 'r', encoding = 'utf-8')
for line in csv.reader(f):
### if you want elements of list ###
l.append(line)
### if you want elements of str ###
# l.append(''.join(line))
f.close()
return l
⑶ 데이터 프레임으로 바꾼 뒤 .csv 파일로 쓰기 : pandas.DataFrame에서 정확한 행/열을 가져올 때 iloc을 사용
# https://pandas.pydata.org/docs/reference/api/pandas.DataFrame.to_csv.html
pandas.DataFrame(MY_VARIABLE).to_csv(FILE_PATH)
⑷ 디렉토리 내 모든 .csv 파일 읽기
import glob
print(glob.glob("./dir/*.csv"))
⑹ 웹사이트 크롤링(crawling) (레퍼런스)
import io
import requests
import pandas as pd
url = 'https://typeset.io/search?q=Microbiome'
github_session = requests.Session()
download = github_session.get(url).content
print(download)
⑺ pdf 파일 합치기 (ref)
from PyPDF2 import PdfWriter
merger = PdfWriter()
for pdf in ['pdf_1.pdf', 'pdf_2.pdf', 'pdf_3.pdf']:
merger.append(pdf)
merger.write(target + ".pdf")
merger.close()
⑻ HTML to MarkDown
!pip install html2text
import html2text
def html_to_markdown(html_content):
# Create an html2text converter object
h = html2text.HTML2Text()
h.ignore_links = False
# Convert the HTML to Markdown
markdown_content = h.handle(html_content)
return markdown_content
# Example Usage
html_code = """
<h1>Hello World</h1>
<p>This is a paragraph. <a href="https://example.com">Here is a link</a>.</p>
"""
markdown_code = html_to_markdown(html_code)
print(markdown_code)
⑼ MarkDown to HTML
import markdown
def md_to_html(md_file_path, html_file_path):
"""
Convert a Markdown file to an HTML file.
:param md_file_path: Path to the input Markdown file.
:param html_file_path: Path to the output HTML file.
"""
# Read the Markdown file
with open(md_file_path, 'r', encoding='utf-8') as file:
md_content = file.read()
# Convert Markdown to HTML
html_content = markdown.markdown(md_content)
# Write the HTML content to a file
with open(html_file_path, 'w', encoding='utf-8') as file:
file.write(html_content)
# Example usage
md_to_html('example.md', 'example.html')
⑽ 주어진 폴더 내 모든 PDF 파일 합치기 (가나다 순)
import os
import glob
import fitz # PyMuPDF library
def merge_pdfs(input_folder, output_path):
# input_folder: PDF 파일들이 있는 디렉토리
# output_path: 결과물 PDF 파일의 경로
# 입력 폴더에서 PDF 파일 목록 가져오기
pdf_files = glob.glob(os.path.join(input_folder, '*.pdf'))
print(pdf_files)
# 가나다 순으로 정렬
pdf_files.sort()
# PyMuPDF의 PdfWriter 객체 생성
pdf_writer = fitz.open()
# 모든 PDF 파일을 합병
for pdf_file in pdf_files:
pdf_document = fitz.open(pdf_file)
for page_num in range(pdf_document.page_count):
page = pdf_document[page_num]
pdf_writer.insert_pdf(pdf_document, from_page=page_num, to_page=page_num)
# 결과물 PDF 파일 저장
pdf_writer.save(output_path)
pdf_writer.close()
# 파일 합병 완료 메시지 출력
print(f'PDF 파일이 {output_path}로 합병되었습니다.')
# 입력 폴더와 결과물 파일 경로 설정
input_folder = r'D:/1'
output_path = r'D:/output.pdf'
# PDF 파일 합병 실행
merge_pdfs(input_folder, output_path)
⑾ 특정 html 문서에서 모든 다운로드 링크를 수집한 뒤 파일 다운로드
import requests
from bs4 import BeautifulSoup
import os
def download_file(url, local_filename):
"""Function to download a file from a given URL."""
with requests.get(url, stream=True) as r:
r.raise_for_status()
with open(local_filename, 'wb') as f:
for chunk in r.iter_content(chunk_size=8192):
f.write(chunk)
return local_filename
# Read the modified HTML file
with open('modified_html_file.html', 'r') as file:
html_content = file.read()
# Parse the HTML
soup = BeautifulSoup(html_content, 'html.parser')
# Find all 'a' tags with href attributes
links = soup.find_all('a', href=True)
# Folder to save files
save_folder = 'out' ## You must make this folder
os.makedirs(save_folder, exist_ok=True)
# Download each file
for link in links:
url = link['href']
filename = os.path.join(save_folder, url.split('/')[-1])
print(f"Downloading {url}...")
download_file(url, filename)
print("Download completed.")
⑿ GIF 파일을 여러 PNG 파일로 쪼개주는 코드
from PIL import Image
import os
def gif_to_png(gif_filename, output_folder):
# Ensure the output folder exists
if not os.path.exists(output_folder):
os.makedirs(output_folder)
# Open the GIF file
with Image.open(gif_filename) as img:
# Loop over each frame in the GIF
for frame in range(img.n_frames):
# Select the frame
img.seek(frame)
# Save the frame as a PNG file
frame_filename = f"{output_folder}/frame_{frame}.png"
img.save(frame_filename)
print(f"Saved {frame_filename}")
# Example usage
gif_filename = 'img.gif' # Replace with your GIF file path
output_folder = 'out' # Folder where PNG files will be saved
gif_to_png(gif_filename, output_folder)
⒀ 디렉토리 트리 구조를 출력하는 코드
import os
def print_tree(directory, prefix=''):
"""Recursively prints a tree diagram of the directory structure."""
files = sorted(os.listdir(directory))
for i, file in enumerate(files):
path = os.path.join(directory, file)
is_last = i == (len(files) - 1)
print(f"{prefix}{'└── ' if is_last else '├── '}{file}")
if os.path.isdir(path):
# Add custom annotations here if file/directory matches certain criteria
new_prefix = prefix + (' ' if is_last else '│ ')
print_tree(path, new_prefix)
# Replace '/path/to/directory' with the actual directory path you want to visualize
print_tree('/path/to/directory')
4. 자료구조 [목차]
⑴ 개요
① 배열
② 연결된 리스트
③ 스택
④ 큐
⑤ 트리
⑥ 그래프
⑦ 해시
⑧ 셋
⑵ counting island 알고리즘 : M × N 리스트인 world에서 1을 땅, 0을 물이라 할 때, 섬의 개수를 세는 함수
def counting_island(world: list)->int:
class Node():
def __init__(self, i, j):
self.i = i
self.j = j
class undirected_graph():
def __init__(self, V:list, E:list)->None:
self.V = V[:]
self.neighbor = {}
for v in V:
self.neighbor[v] = []
for (v,w) in E:
self.neighbor[v].append(w)
def DFT_preorder(self)->int:
count = 0
if self.V:
visited = {}
for v in self.V:
visited[v]=False
for v in self.V:
if not visited[v]:
count += 1
self.__DFT__preorderHelp(visited, v)
return count
def __DFT__preorderHelp(self, visited: list, v: int)->None:
if not visited[v]:
visited[v] = True
for w in self.neighbor[v]:
self.__DFT__preorderHelp(visited, w)
V = []
E = []
for i in range(len(world)):
for j in range(len(world[0])):
if world[i][j] == 1:
V.append(Node(i, j))
for v in V:
for w in V:
if w.i == v.i and w.j == v.j - 1:
E.append((v,w))
if w.i == v.i and w.j == v.j + 1:
E.append((v,w))
if w.i == v.i - 1 and w.j == v.j:
E.append((v,w))
if w.i == v.i + 1 and w.j == v.j:
E.append((v,w))
g = undirected_graph(V, E)
return g.DFT_preorder()
world1 = [[1,1,1,1,0], [1,0,0,1,0], [1,1,0,1,0], [1,1,0,0,0]]
counting_island(world1) # 1
world2 = [[1,1,0,0,0], [1,1,0,0,0], [0,0,1,1,0], [0,0,0,0,1]]
counting_island(world2) # 3
world3 = [[0,1,0,1,0,1]]
counting_island(world3) # 3
5. 이미지 처리 [목차]
① x, y가 주어졌을 때 scatter plot을 그리는 함수
plt.scatter(x, y, alpha = 0.01)
plt.xlabel('brightness of img1')
plt.ylabel('brightness of img2')
② 주어진 이미지의 히스토그램을 그리는 함수
import numpy as np
import cv2
import matplotlib.pyplot as plt
img = cv2.imread('image.png')
fig, axes = plt.subplots(1, 1)
axes.hist(img.ravel(), bins=20)
axes.set_title('Histogram')
⑵ 이미지 저장
① 이미지를 png로 저장하는 예시 (ref)
import matplotlib.pyplot as plt
fig = plt.figure(figsize=(5, 5))
fig.patch.set_visible(False)
plt.imshow(demask_image_t[0], interpolation='nearest')
plt.axis('off')
plt.savefig('foo.png', bbox_inches='tight', dpi = 300)
② 이미지를 pdf로 저장하는 예시
...
plt.show()
fig.savefig('foo.pdf', bbox_inches='tight', dpi = 300)
⑶ cv2 이미지 RGB 컬러 재배열
import cv2
d = cv2.imread("/home/data/ST/WuSZ_2021_NG_TNBC/GSE/1160920F_spatial/spatial/tissue_hires_image.png")
d_array = cv2.cvtColor(d, cv2.COLOR_BGR2RGB)
plt.imshow(d_array)
⑷ cv2 이미지 resize : 예를 들어 img가 (1024, 1024, 3)이라면, img_re는 (512, 512, 3)이 됨
img_re = cv2.resize(img, dsize = (512, 512))
⑸ RGB 이미지를 흑백 이미지로 변환
## version 1.
img = cv2.cvtColor(img, cv2.COLOR_BGR2GRAY)
## version 2
import numpy as np
def RGBtoGray(img):
out = np.empty((img.shape[0], img.shape[1]))
for i in range(img.shape[0]):
for j in range(img.shape[1]):
out[i:i+1, j:j+1] = ( 0.2989*img[i:i+1, j:j+1, 0:1] +
0.5870*img[i:i+1, j:j+1, 1:2] +
0.1140*img[i:i+1, j:j+1, 2:3]
).item()
return out
⑹ 3-channel RGB 이미지에서 red image(1 × W × H)를 2차원 이미지(W × H)로 만드는 함수
img_ = img[:,:,0:1].reshape(img.shape[0], img.shape[1])
⑺ 이미지에서 특정 값을 다른 값으로 바꾸는 함수
def recolor(img, pre, post):
for i in range(img.shape[0]):
for j in range(img.shape[1]):
if img[i:i+1, j:j+1] == pre:
img[i:i+1, j:j+1] = post
return(img)
⑻ 정수형 numpy.ndarray 변수를 실수형 numpy.ndarray 변수로 바꾸기 (레퍼런스)
import cv2
import numpy as np
import matplotlib.pyplot as plt
img = cv2.imread('img.png')
img_cvt = np.array(img[:,:,:], dtype=np.float64)
⑼ 한 이미지에서 red와 green의 상관관계
import cv2
import matplotlib.pyplot as plt
from skimage.util import view_as_windows
import numpy as np
import scipy.stats
def two_image_correlation_RG(img1_dir):
img1 = cv2.imread(img1_dir) # RGB image
img1 = cv2.cvtColor(img1, cv2.COLOR_BGR2RGB)
l_img1 = []
l_img2 = []
for i in range(img1.shape[0]):
for j in range(img1.shape[1]):
l_img1.append((
img1[i:i+1, j:j+1, 0:1]
).item())
l_img2.append((
img1[i:i+1, j:j+1, 1:2]
).item())
print("brightness of img1")
print(np.mean(l_img1))
print("brightness of img2")
print(np.mean(l_img2))
print("img1-img2 correlation")
print(scipy.stats.pearsonr(l_img1, l_img2) )
plt.scatter(l_img1, l_img2, alpha = 0.01)
plt.xlabel('brightness of img1')
plt.ylabel('brightness of img2')
⑽ 이미지 간 상관관계
import cv2
import matplotlib.pyplot as plt
from skimage.util import view_as_windows
import numpy as np
import scipy.stats
def two_image_correlation(img1_dir, img2_dir):
# img1 and img2 should be same in size
img1 = cv2.imread(img1_dir) # RGB image
img1 = cv2.cvtColor(img1, cv2.COLOR_BGR2RGB)
img2 = cv2.imread(img2_dir) # RGB image
img2 = cv2.cvtColor(img2, cv2.COLOR_BGR2RGB)
l_img1 = []
l_img2 = []
for i in range(img1.shape[0]):
for j in range(img1.shape[1]):
l_img1.append((
0.2989*img1[i:i+1, j:j+1, 0:1] +
0.5870*img1[i:i+1, j:j+1, 1:2] +
0.1140*img1[i:i+1, j:j+1, 2:3]
).item())
l_img2.append((
0.2989*img2[i:i+1, j:j+1, 0:1] +
0.5870*img2[i:i+1, j:j+1, 1:2] +
0.1140*img2[i:i+1, j:j+1, 2:3]
).item())
print("brightness of img1")
print(np.mean(l_img1))
print("brightness of img2")
print(np.mean(l_img2))
print("img1-img2 correlation")
print(scipy.stats.pearsonr(l_img1, l_img2) )
plt.scatter(l_img1, l_img2, alpha = 0.05)
plt.xlabel('brightness of img1')
plt.ylabel('brightness of img2')
# sns.regplot(l_b_CD31, l_b_Lipo, alpha = 0.05)
⑾ 한 3차원 이미지에서 red와 green의 상관관계
import cv2
import numpy as np
import matplotlib.pyplot as plt
from skimage.util import view_as_windows
import scipy.stats
import glob
def two_image_correlation_RG_3D(my_dir):
images = glob.glob(my_dir + "*.jpg")
l_img1 = []
l_img2 = []
for k in range(len(images)):
print(k)
img1 = cv2.imread(images[k])
img1 = cv2.cvtColor(img1, cv2.COLOR_BGR2RGB)
for i in range(img1.shape[0]):
for j in range(img1.shape[1]):
if (img1[i:i+1, j:j+1, 0:1] + img1[i:i+1, j:j+1, 1:2] + img1[i:i+1, j:j+1, 2:3]) != 0:
l_img1.append((
img1[i:i+1, j:j+1, 0:1]
).item())
l_img2.append((
img1[i:i+1, j:j+1, 1:2]
).item())
print("brightness of img1")
print(np.mean(l_img1))
print("brightness of img2")
print(np.mean(l_img2))
print("img1-img2 correlation")
print(scipy.stats.pearsonr(l_img1, l_img2) )
plt.scatter(l_img1, l_img2, alpha = 0.01)
plt.xlabel('brightness of img1')
plt.ylabel('brightness of img2')
⑿ 한 쌍의 이미지의 SSIM 값을 구하는 코드
def SSIM(x, y):
# assumption : x and y are grayscale images with the same dimension
import numpy as np
def mean(img):
return np.mean(img)
def sigma(img):
return np.std(img)
def cov(img1, img2):
img1_ = np.array(img1[:,:], dtype=np.float64)
img2_ = np.array(img2[:,:], dtype=np.float64)
return np.mean(img1_ * img2_) - mean(img1) * mean(img2)
K1 = 0.01
K2 = 0.03
L = 256 # when each pixel spans 0 to 255
C1 = K1 * K1 * L * L
C2 = K2 * K2 * L * L
C3 = C2 / 2
l = (2 * mean(x) * mean(y) + C1) / (mean(x)**2 + mean(y)**2 + C1)
c = (2 * sigma(x) * sigma(y) + C2) / (sigma(x)**2 + sigma(y)**2 + C2)
s = (cov(x, y) + C3) / (sigma(x) * sigma(y) + C3)
return l * c * s
⒀ 한 쌍의 이미지의 mutual information 값을 구하는 코드 (레퍼런스)
def mutual_information(img1, img2):
import numpy as np
import cv2
import matplotlib.pyplot as plt
# img1 and img2 are 3-channel color images
a = img1[:,:,0:1].reshape(img1.shape[0], img1.shape[1])
b = img2[:,:,0:1].reshape(img2.shape[0], img2.shape[1])
hgram, x_edges, y_edges = np.histogram2d(
a.ravel(),
b.ravel(),
bins=20
)
pxy = hgram / float(np.sum(hgram))
px = np.sum(pxy, axis=1) # marginal for x over y
py = np.sum(pxy, axis=0) # marginal for y over x
px_py = px[:, None] * py[None, :] # Broadcast to multiply marginals
nzs = pxy > 0 # Only non-zero pxy values contribute to the sum
return np.sum(pxy[nzs] * np.log(pxy[nzs] / px_py[nzs]))
⒁ 회귀곡선을 구하는 코드
from sklearn import linear_model
reg = linear_model.LinearRegression()
reg.fit([[0,0], [1,1], [2,2]], [0, 1, 2])
# LinearRegression()
reg.coef_
# array([0.5, 0.5])
⒂ 공간전사체(ST)에서 배경 이미지, x 좌표, y 좌표, 컬러 c가 주어졌을 때 spot mapping image 생성 (레퍼런스)
def spatial_featuremap(img, x, y, c):
tsimg = np.zeros(img.shape[:2])
tsimg_row = y # np.array형 변수
tsimg_col = x # np.array형 변수
for rr, cc, t in zip(tsimg_row, tsimg_col, c):
r, c = draw.circle(rr, cc, radius = 2.5)
tsimg[r,c]= t
return tsimg
⒃ 이미지의 양각(embossing), 음각(intaglio)을 판단하는 함수 : return 값 (-1 ~ 1)이 양수이면 양각, 음수이면 음각
def is_embossing(image):
l_1 = []
l_2 = []
row_cm = image.shape[0]/2
col_cm = image.shape[1]/2
def distance(x:int, y:int):
import numpy as np
return np.sqrt(x*x + y*y)
def my_sqrt(x:int, y:int, z:int):
import numpy as np
return np.sqrt(x*x + y*y + z*z)
for i in range(image.shape[0]):
for j in range(image.shape[1]):
l_1.append( distance(i - row_cm, j - col_cm ))
if len(image.shape) == 2: # grayscale
l_2.append( image[i:i+1, j:j+1].item() )
elif len(image.shape) == 3: # 3-channel color image
l_2.append(
my_sqrt( image[i:i+1, j:j+1, 0:1].item(),
image[i:i+1, j:j+1, 1:2].item(),
image[i:i+1, j:j+1, 2:3].item()
)
)
print("Distance from Center")
print(np.mean(l_1))
print("Pixel Intensity")
print(np.mean(l_2))
plt.scatter(l_1, l_2, alpha = 0.01)
plt.ylim(0, 255)
plt.xlabel('Distance from Center')
plt.ylabel('Pixel Intensity')
return scipy.stats.pearsonr(l_1, l_2)[0] * (-1)
⒄ 여러 이미지를 합쳐서 하나의 이미지로 표현하는 유용한 코드
fig, axes = plt.subplots(2,2,figsize=(6,20))
sns.barplot(df1[0:20], x='Gene', y ='Enrichment', ax = axes[0][0])
axes[0][0].tick_params(axis='x', rotation=90)
axes[0][0].set_title('DataFrame 1')
sns.barplot(df2[0:20], x='Gene', y ='Enrichment', ax = axes[0][1])
axes[0][1].tick_params(axis='x', rotation=90)
axes[0][1].set_title('DataFrame 2')
sns.barplot(df3[0:20], x='Gene', y ='Enrichment', ax = axes[1][0])
axes[1][0].tick_params(axis='x', rotation=90)
axes[1][0].set_title('DataFrame 3')
sns.barplot(df4[0:20], x='Gene', y ='Enrichment', ax = axes[1][1])
axes[1][1].tick_params(axis='x', rotation=90)
axes[1][1].set_title('DataFrame 4')
plt.tight_layout()
plt.show()
⒅ 이미지의 base64 코드가 잘린 경우 부분 복호화하는 코드
import base64
from PIL import Image, ImageFile
import io
# if the data is <img src="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAA+0AA..."
data = "iVBORw0KGgoAAAANSUhEUgAAA+0AA..." # you need to modify this part
# If the length of the data is 'num' more than a multiple of 4, trim the last character(s)
num = len(data) % 4
data = data[:-num]
# Add padding to ensure the length is a multiple of 4
padding = '=' * ((4 - len(data) % 4) % 4)
data = data + padding
try:
decoded_data = base64.b64decode(data)
# Process the decoded data as needed
except Exception as e:
print("Error in decoding base64:", e)
image = Image.open(io.BytesIO(decoded_data))
ImageFile.LOAD_TRUNCATED_IMAGES = True
try:
image = Image.open(io.BytesIO(decoded_data))
image.show()
except IOError:
print("Cannot open the image.")
⒆ chart-to-text (ref)
⒇ 주어진 이미지와 동일한 사이즈의 random image 생성하기
import numpy as np
import cv2
# Load the image using OpenCV
tsimg = cv2.imread(imgfile)
# Get the dimensions of the original image
height, width, channels = tsimg.shape
# Create a random image with the same dimensions
# Random values are generated in the range 0-255, which is the range for pixel values in an 8-bit image
random_img = np.random.randint(0, 256, (height, width, channels), dtype=np.uint8)
# Optionally, you can save or display the random image using OpenCV
cv2.imwrite('random_image.png', random_img) # Save the random image
6. 데이터 사이언스 [목차]
⑴ K means clustering
from sklearn.cluster import KMeans
X = [[1, 2, 3],[1, 2, 3.1],[2, 2, 4],[2, 2, 4.1]]
kmeans = KMeans(n_clusters=2, random_state=0)
kmeans.fit(X)
cluster_labels = kmeans.labels_
print(cluster_labels)
# [1 1 0 0]
7. 딥러닝 함수 [목차]
⑴ 딥러닝 예제 : MNIST (즉, 손으로 쓴 숫자들) 데이터에 딥러닝 모델 적용하기
import tensorflow as tf
from tensorflow.keras import layers, models
# Load the MNIST dataset
mnist = tf.keras.datasets.mnist
(train_images, train_labels), (test_images, test_labels) = mnist.load_data()
# Normalize the pixel values of the images to be between 0 and 1
train_images, test_images = train_images / 255.0, test_images / 255.0
# Define a simple sequential model
def create_model():
model = models.Sequential([
layers.Flatten(input_shape=(28, 28)), # Flatten the 2D image to a 1D array
layers.Dense(128, activation='relu'), # First hidden layer with 128 neurons and ReLU activation
layers.Dropout(0.2), # Dropout layer to reduce overfitting
layers.Dense(10, activation='softmax') # Output layer with 10 neurons for 10 classes and softmax activation
])
return model
# Create the model
model = create_model()
# Compile the model
model.compile(optimizer='adam',
loss='sparse_categorical_crossentropy',
metrics=['accuracy'])
# Train the model
model.fit(train_images, train_labels, epochs=5)
# Evaluate the model
test_loss, test_acc = model.evaluate(test_images, test_labels)
print(f'Test accuracy: {test_acc}')
⑵ 6만 개의 데이터 Xtr, 6만 개의 레이블 Ytr이 있을 때, 1만 개의 Xte를 KNN으로 분류하는 알고리즘
import tensorflow as tf
(Xtr, Ytr), (Xte, Yte) = tf.keras.datasets.mnist.load_data()
print(Xtr.shape) # (60000, 28, 28)
print(Ytr.shape) # (60000,)
print(Xte.shape) # (10000, 28, 28)
print(Yte.shape) # (10000,)
Xtr_rows = Xtr.reshape(Xtr.shape[0], 28*28)
Xte_rows = Xte.reshape(Xte.shape[0], 28*28)
print(Xtr_rows.shape) # (60000, 784)
print(Xte_rows.shape) # (10000, 784)
def KNN_predict(Xtr_rows, Ytr, Xte_rows, dist_metric='L2'):
import numpy as np
class NearestNeighbor(object):
def __init__(self):
pass
def train(self, X, Y):
self.Xtr = X
self.Ytr = Y
def predict(self, X, dist_metric=dist_metric):
num_test = X.shape[0]
Ypred = np.zeros(num_test, dtype = self.Ytr.dtype)
for i in range(num_test):
if dist_metric=='L1': ## L1 distance
distances = np.sum(np.abs(self.Xtr - X[i, :]), axis = 1)
elif dist_metric=='L2': ## L2 distance
distances = np.sum(np.square(self.Xtr - X[i, :]), axis = 1)
elif dist_metric=='dot': ## dot distance
distances = np.dot(self.Xtr, X[i, :])
min_index = np.argmin(distances)
Ypred[i] = self.Ytr[min_index]
if i%100 == 0:
print(i)
return Ypred
nn = NearestNeighbor()
nn.train(Xtr_rows, Ytr)
Yte_predict = nn.predict(Xte_rows, dist_metric)
return Yte_predict
def KNN_evaluate(Xtr_rows, Ytr, Xte_rows, Yte, dist_metric='L2'):
Yte_predict = KNN_predict(Xtr_rows, Ytr, Xte_rows, dist_metric)
print ('accuracy: %f' + str(np.mean(Yte_predict == Yte)) )
# L1 : accuracy = 47.29%
# L2 : accuracy = 27.24%
# dot : accuracy = 9.9%
KNN_evaluate(Xtr_rows, Ytr, Xte_rows, Yte)
⑶ 1D CNN으로 구현한 binary classifier 함수
# reference : https://wikidocs.net/80783
def binary_predict_by_1D_CNN (Xtr_rows, Ytr, Xte_rows, Yte):
from tensorflow.keras.models import Sequential
from tensorflow.keras.layers import Embedding, Dropout, Conv1D, GlobalMaxPooling1D, Dense
from tensorflow.keras.callbacks import EarlyStopping, ModelCheckpoint
from tensorflow.keras.models import load_model
vocab_size = 10000
embedding_dim = 256 # 임베딩 벡터의 차원
dropout_ratio = 0.3 # 드롭아웃 비율
num_filters = 256 # 커널의 수
kernel_size = 3 # 커널의 크기
hidden_units = 128 # 뉴런의 수
model = Sequential()
model.add(Embedding(vocab_size, embedding_dim))
model.add(Dropout(dropout_ratio))
model.add(Conv1D(num_filters, kernel_size, padding='valid', activation='relu'))
model.add(GlobalMaxPooling1D())
model.add(Dense(hidden_units, activation='relu'))
model.add(Dropout(dropout_ratio))
model.add(Dense(1, activation='sigmoid'))
model.summary()
es = EarlyStopping(monitor='val_loss', mode='min', verbose=1, patience=3)
mc = ModelCheckpoint('best_model.h5', monitor='val_acc', mode='max', verbose=1, save_best_only=True)
model.compile(optimizer='adam', loss='binary_crossentropy', metrics=['acc'])
history = model.fit(Xtr_rows, Ytr, epochs=20, validation_data=(Xte_rows, Yte), callbacks=[es, mc])
def binary_evaluate_by_1D_CNN(Xtr_rows, Ytr, Xte_rows, Yte):
from tensorflow.keras.models import load_model
binary_predict_by_1D_CNN(Xtr_rows, Ytr, Xte_rows, Yte)
loaded_model = load_model('best_model.h5')
print("\n 테스트 정확도: %.4f" % (loaded_model.evaluate(Xte_rows, Yte)[1]))
##################
# Example 1. Mnist
import tensorflow as tf
(Xtr, Ytr), (Xte, Yte) = tf.keras.datasets.mnist.load_data()
Xtr_rows = Xtr.reshape(Xtr.shape[0], 28*28)
Xte_rows = Xte.reshape(Xte.shape[0], 28*28)
print(Xtr_rows.shape) # (60000, 784)
print(Ytr.shape) # (60000,)
print(Xte_rows.shape) # (10000, 784)
print(Yte.shape) # (10000,)
binary_evaluate_by_1D_CNN(Xtr_rows, Ytr > 5, Xte_rows, Yte > 5)
# 1D CNN accuracy : 7.82%
##################
# Example 2. IMDB
from tensorflow.keras import datasets
from tensorflow.keras.preprocessing.sequence import pad_sequences
vocab_size = 10000
(X_train, y_train), (X_test, y_test) = datasets.imdb.load_data(num_words=vocab_size)
max_len = 200
X_train = pad_sequences(X_train, maxlen=max_len)
X_test = pad_sequences(X_test, maxlen=max_len)
print(X_train.shape)
print(y_train.shape)
print(X_test.shape)
print(y_test.shape)
binary_evaluate_by_1D_CNN(X_train, y_train, X_test, y_test)
# 1D CNN accuracy : 88.92%
⑷ 임의의 이미지로부터 pre-trained CNN을 통해 512차원 feature를 추출하는 함수
# reference
## https://github.com/mexchy1000/spade/blob/master/spade_spatial_marker_by_deeplearning.py
import os
import numpy as np
import matplotlib.pyplot as plt
from skimage import draw
import pandas as pd
import argparse
from keras import backend as K
from keras.applications import vgg16, resnet50, inception_v3
from sklearn.manifold import TSNE
from sklearn.decomposition import PCA
K.set_image_data_format='channels_last'
os.environ['KERAS_BACKEND'] = 'tensorflow'
def features_512D_from_image_by_CNN (img, model_name = 'VGG16'):
# Image Patch
img_re = cv2.resize(img, dsize = (32, 32))
tspatches = []
tspatches.append(img_re)
tspatches.append(img_re) # intentional duplicate
tspatches = np.asarray(tspatches)
# Pretrained model
if model_name == 'VGG16':
pretrained_model = vgg16.VGG16(weights='imagenet', include_top = False, pooling='avg', input_shape = (32,32,3))
X_in = tspatches.copy()
X_in = vgg16.preprocess_input(X_in)
elif model_name == 'ResNet50':
pretrained_model = resnet50.ResNet50(weights='imagenet', include_top = False, pooling='avg', input_shape = (32,32,3))
X_in = tspatches.copy()
X_in = resnet50.preprocess_input(X_in)
elif model_name == 'InceptionV3':
# 아래 코드에서 input_shape를 75 이상으로 늘리지 않으면 에러가 남
pretrained_model = inception_v3.InceptionV3(weights='imagenet', include_top = False, pooling='avg', input_shape = (32,32,3))
X_in = tspatches.copy()
X_in = inception_v3.preprocess_input(X_in)
pretrained_model.trainable = False
pretrained_model.summary()
# Get the features
ts_features = pretrained_model.predict(X_in)
return ts_features[0]
⑸ 임의의 가변 길이 자연어 문장을 그 의미를 고려하여 384차원으로 만드는 함수 (cf. CELLama)
from langchain.embeddings.sentence_transformer import SentenceTransformerEmbeddings
import numpy as np
from scipy.sparse import csr_matrix
import pandas as pd
from sklearn.neighbors import NearestNeighbors
import torch
from torch.utils.data import DataLoader, TensorDataset
from xgboost import XGBClassifier
def sentences_to_embedding(sentences):
embedding_function = SentenceTransformerEmbeddings(model_name="all-MiniLM-L6-v2")
db = embedding_function.embed_documents(sentences)
emb_res = np.asarray(db)
return emb_res
sentences = []
sentences.append("What is the meaning of: obsolete")
sentences.append("What is the meaning of: old-fashioned")
sentences.append("What is the meaning of: demagogue")
emb_res = sentences_to_embedding(sentences)
8. 예외 처리 [목차]
⑴ 기본적인 예외 처리 구문
try:
raise KeyError("Error")
except:
print("An exception occurred")
# An exception occurred
⑵ error 메시지 출력 (ref.)
try:
print(1/0)
except Exception as e:
print(e)
9. 생물정보학 [목차]
⑴ highly variable gene을 구하는 코드
import scanpy as sc
tissue_dir = './outs'
adata1 = sc.read_visium(tissue_dir)
sc.set_figure_params(facecolor="white", figsize=(8, 8))
sc.settings.verbosity = 3
adata1.var_names_make_unique()
sc.pp.normalize_total(adata1, inplace=True)
sc.pp.log1p(adata1)
sc.pp.highly_variable_genes(adata1, flavor="seurat", n_top_genes=200)
gene_list=adata1.var.loc[adata1.var.highly_variable==True,:].index
⑵ highest expressing gene을 구하는 코드
import scanpy as sc
import numpy as np
import pandas as pd
pbmc = sc.read_h5ad("Tabula_Sapiens.h5ad")
# normalize counts matrix so that each 'cell' (barcode) has counts summing to 1
pbmc.X_norm = sc.pp.normalize_total(pbmc, target_sum=1, inplace=False)['X']
# create new adata.var column contaning mean of each column of adata.X_norm above
# this is total normalized counts per gene a.k.a. 'mean_total_expression'
pbmc.var['mean_expression'] = np.ravel(pbmc.X_norm.mean(0))
# return pd.DataFrame of n top-ranked genes by mean expression
x = pd.DataFrame(pbmc.var.nlargest(200, 'mean_expression')['mean_expression'])
⑶ GO plot 그리는 법 (ver. 1) (비추천)
# Reference
## https://github.com/mousepixels/sanbomics_scripts/blob/main/GO_in_python.ipynb
## https://snyk.io/advisor/python/goatools/functions/goatools.anno.genetogo_reader.Gene2GoReader
def GO(markers, max_terms = 6):
# type(markers) = numpy.ndarray
# dtype = object
if len(markers) == 0:
return
from genes_ncbi_mus_musculus_proteincoding import GENEID2NT as GeneID2nt_mus
from genes_ncbi_homo_sapiens_proteincoding import GENEID2NT as GeneID2nt_homo
from goatools.base import download_go_basic_obo
from goatools.base import download_ncbi_associations
from goatools.obo_parser import GODag
from goatools.anno.genetogo_reader import Gene2GoReader
from goatools.goea.go_enrichment_ns import GOEnrichmentStudyNS
obo_fname = download_go_basic_obo()
fin_gene2go = download_ncbi_associations()
obodag = GODag("go-basic.obo")
#run one time to initialize
mapper = {}
if markers[0] == markers[0].upper(): # Homo sapiens
for key in GeneID2nt_homo:
mapper[GeneID2nt_homo[key].Symbol] = GeneID2nt_homo[key].GeneID
else: # Mus musculus
for key in GeneID2nt_mus:
mapper[GeneID2nt_mus[key].Symbol] = GeneID2nt_mus[key].GeneID
inv_map = {v: k for k, v in mapper.items()}
if markers[0] == markers[0].upper():
objanno = Gene2GoReader(fin_gene2go, taxids=[9606])
else:
objanno = Gene2GoReader(fin_gene2go, taxids=[10090])
ns2assoc = objanno.get_ns2assc()
goeaobj = ''
if markers[0] == markers[0].upper():
goeaobj = GOEnrichmentStudyNS(
GeneID2nt_homo.keys(), # List of human protein-coding genes
ns2assoc, # geneid/GO associations
obodag, # Ontologies
propagate_counts = False,
alpha = 0.05, # default significance cut-off
methods = ['fdr_bh']) # defult multipletest correction method
else:
goeaobj = GOEnrichmentStudyNS(
GeneID2nt_mus.keys(), # List of mouse protein-coding genes
ns2assoc, # geneid/GO associations
obodag, # Ontologies
propagate_counts = False,
alpha = 0.05, # default significance cut-off
methods = ['fdr_bh']) # defult multipletest correction method
GO_items = []
temp = goeaobj.ns2objgoea['BP'].assoc
for item in temp:
GO_items += temp[item]
temp = goeaobj.ns2objgoea['CC'].assoc
for item in temp:
GO_items += temp[item]
temp = goeaobj.ns2objgoea['MF'].assoc
for item in temp:
GO_items += temp[item]
def go_it(test_genes):
print(f'input genes: {len(test_genes)}')
mapped_genes = []
for gene in test_genes:
try:
mapped_genes.append(mapper[gene])
except:
pass
print(f'mapped genes: {len(mapped_genes)}')
goea_results_all = goeaobj.run_study(mapped_genes)
goea_results_sig = [r for r in goea_results_all if r.p_fdr_bh < 0.05]
GO = pd.DataFrame(list(map(lambda x: [x.GO, x.goterm.name, x.goterm.namespace, x.p_uncorrected, x.p_fdr_bh,\
x.ratio_in_study[0], x.ratio_in_study[1], GO_items.count(x.GO), list(map(lambda y: inv_map[y], x.study_items)),\
], goea_results_sig)), columns = ['GO', 'term', 'class', 'p', 'p_corr', 'n_genes',\
'n_study', 'n_go', 'study_genes'])
GO = GO[GO.n_genes > 1]
return GO
df = go_it(markers)
df['per'] = df.n_genes/df.n_go
if df.shape[0] > 0:
df = df.sort_values(by=['p_corr'], axis=0, ascending=True)
if df.shape[0] > max_terms:
df = df[0:max_terms]
import matplotlib.pyplot as plt
import matplotlib as mpl
from matplotlib import cm
import seaborn as sns
import textwrap
fig, ax = plt.subplots(figsize = (0.5, 2.75))
cmap = mpl.cm.bwr_r
norm = mpl.colors.Normalize(vmin = df.p_corr.min(), vmax = df.p_corr.max())
mapper = cm.ScalarMappable(norm = norm, cmap = cm.bwr_r)
cbl = mpl.colorbar.ColorbarBase(ax, cmap = cmap, norm = norm, orientation = 'vertical')
plt.figure(figsize = (2,4))
ax = sns.barplot(data = df, x = 'per', y = 'term', palette = mapper.to_rgba(df.p_corr.values))
ax.set_yticklabels([textwrap.fill(e, 22) for e in df['term']])
plt.show()
⑷ GO plot 그리는 법 (ver. 2) (추천)
def GO(gene_list):
# reference : https://gseapy.readthedocs.io/en/latest/gseapy_example.html
import gseapy
from gseapy import barplot, dotplot
if gene_list[0] == gene_list[0].upper():
enr = gseapy.enrichr(gene_list=gene_list, # or "./tests/data/gene_list.txt",
gene_sets=['GO_Biological_Process_2018','GO_Cellular_Component_2018', 'GO_Molecular_Function_2018'],
organism='human', # don't forget to set organism to the one you desired! e.g. Yeast
outdir=None, # don't write to disk
)
else:
enr = gseapy.enrichr(gene_list=gene_list, # or "./tests/data/gene_list.txt",
gene_sets=['GO_Biological_Process_2018','GO_Cellular_Component_2018', 'GO_Molecular_Function_2018'],
organism='mouse', # don't forget to set organism to the one you desired! e.g. Yeast
outdir=None, # don't write to disk
)
try:
ax = dotplot(enr.results,
column="Adjusted P-value",
x='Gene_set', # set x axis, so you could do a multi-sample/library comparsion
size=10,
top_term=5,
figsize=(3,5),
title = "GO plot",
xticklabels_rot=45, # rotate xtick labels
show_ring=True, # set to False to revmove outer ring
marker='o',
)
except:
print("ValueError: Warning: No enrich terms when cutoff = 0.05")
① gseapy는 plt.subplot과 호환되지 않는 것으로 보임
⑸ convert from ensembl.gene to gene.symbol (표를 이용한 방식)
def ensembl_to_gene(ensembl_list):
ar = []
human = pd.read_csv("https://blog.kakaocdn.net/dn/29YTj/btrS5iG9QOH/Di6RQKxHOPDii7EjkdHN30/human_genes_36601.tsv?attach=1&knm=tfile.tsv", sep = '\t', header = None)
mouse = pd.read_csv("https://blog.kakaocdn.net/dn/wkjwJ/btrS1QSgrpD/VS8ELANCQyeZAA3vL8JQP0/mouse_genes_32285.tsv?attach=1&knm=tfile.tsv", sep = '\t', header = None)
for i in range(len(ensembl_list)):
if 'ENSG' in ensembl_list[i]: # human gene
index = human[0].tolist().index(ensembl_list[i])
ar.append(human[1][index])
elif 'ENSMUSG' in ensembl_list[i]: # mouse gene
index = mouse[0].tolist().index(ensembl_list[i])
ar.append(mouse[1][index])
return(ar)
⑹ convert from gene.symbol to ensembl.gene (표를 이용한 방식)
def gene_to_ensembl(gene_list):
ar = []
human = pd.read_csv("https://blog.kakaocdn.net/dn/29YTj/btrS5iG9QOH/Di6RQKxHOPDii7EjkdHN30/human_genes_36601.tsv?attach=1&knm=tfile.tsv", sep = '\t', header = None)
mouse = pd.read_csv("https://blog.kakaocdn.net/dn/wkjwJ/btrS1QSgrpD/VS8ELANCQyeZAA3vL8JQP0/mouse_genes_32285.tsv?attach=1&knm=tfile.tsv", sep = '\t', header = None)
for i in range(len(gene_list)):
if gene_list[i] == gene_list[i].upper(): # human gene
index = human[1].tolist().index(gene_list[i])
ar.append(human[0][index])
else: # mouse gene
index = mouse[1].tolist().index(gene_list[i])
ar.append(mouse[0][index])
return(ar)
⑺ human 유전자, mouse 유전자 상호 간 변환
import pandas as pd
import numpy as np
def find_idx(my_list, e):
for i in range(len(my_list)):
if my_list[i] == e:
return i
return -1
def human_to_mouse(human_gene:list):
hom = pd.read_csv("https://blog.kakaocdn.net/dn/cVeqsA/btrS1JMnxyX/HtVhPmqtxdgt7LQlGkeql0/HOM_MouseHumanSequence.csv?attach=1&knm=tfile.csv")
mouse_gene = []
for i in range(len(human_gene)):
index = find_idx(hom['Symbol'], human_gene[i])
DB_Class_Key = hom['DB Class Key'][index]
hom_ = hom[hom['DB Class Key'] == DB_Class_Key]
hom__ = hom_[hom_['Common Organism Name'] == 'mouse, laboratory']
mouse_gene.append(np.array(hom__['Symbol'])[0])
return mouse_gene
def mouse_to_human(mouse_gene:list):
hom <- pd.read_csv("https://blog.kakaocdn.net/dn/cVeqsA/btrS1JMnxyX/HtVhPmqtxdgt7LQlGkeql0/HOM_MouseHumanSequence.csv?attach=1&knm=tfile.csv")
human_gene = []
for i in range(len(mouse_gene)):
index = find_idx(hom['Symbol'], mouse_gene[i])
DB_Class_Key = hom['DB Class Key'][index]
hom_ = hom[hom['DB Class Key'] == DB_Class_Key]
hom__ = hom_[hom_['Common Organism Name'] == 'human']
mouse_gene.append(np.array(hom__['Symbol'])[0])
return human_gene
⑻ tissue_dir 디렉토리 내 matrix.mtx.gz, barcodes.tsv, features.tsv 및 spatial 폴더가 있을 때, Visium 데이터를 Python 상에서 읽는 코드
import scanpy as sc
import pandas as pd
import matplotlib.pyplot as plt
from matplotlib.image import imread
import numpy as np
import cv2
import math
from pathlib import Path, PurePath
from typing import Union, Dict, Optional, Tuple, BinaryIO
import json
def to_spatial(adata, path, library_id = 'TNBC1'):
adata.uns["spatial"][library_id] = dict()
path = Path(path)
files = dict(
tissue_positions_file=path / 'spatial/tissue_positions_list.csv',
scalefactors_json_file=path / 'spatial/scalefactors_json.json',
hires_image=path / 'spatial/tissue_hires_image.png',
lowres_image=path / 'spatial/tissue_lowres_image.png',
)
# check if files exists, continue if images are missing
for f in files.values():
if not f.exists():
if any(x in str(f) for x in ["hires_image", "lowres_image"]):
logg.warning(
f"You seem to be missing an image file.\n"
f"Could not find '{f}'."
)
else:
raise OSError(f"Could not find '{f}'")
adata.uns["spatial"][library_id]['images'] = dict()
for res in ['hires', 'lowres']:
try:
adata.uns["spatial"][library_id]['images'][res] = imread(
str(files[f'{res}_image'])
)
except Exception:
raise OSError(f"Could not find '{res}_image'")
# read json scalefactors
adata.uns["spatial"][library_id]['scalefactors'] = json.loads(
files['scalefactors_json_file'].read_bytes()
)
#adata.uns["spatial"][library_id]["metadata"] = {
# k: (str(attrs[k], "utf-8") if isinstance(attrs[k], bytes) else attrs[k])
# for k in ("chemistry_description", "software_version")
# if k in attrs
#}
# read coordinates
positions = pd.read_csv(files['tissue_positions_file'], header=None)
positions.columns = [
'barcode',
'in_tissue',
'array_row',
'array_col',
'pxl_col_in_fullres',
'pxl_row_in_fullres',
]
positions.index = positions['barcode']
adata.obs = adata.obs.join(positions, how="left")
adata.obsm['spatial'] = adata.obs[
['pxl_row_in_fullres', 'pxl_col_in_fullres']
].to_numpy()
adata.obs.drop(
columns=['barcode', 'pxl_row_in_fullres', 'pxl_col_in_fullres'],
inplace=True,
)
return adata
def load_adata(tissue_dir):
adata1 = sc.read_mtx(tissue_dir + 'matrix.mtx')
adata1 = adata1.transpose()
cellname = pd.read_csv(tissue_dir + 'barcodes.tsv', sep="\t", header=None, index_col=1, names=['idx', 'barcode'])
cellname.index = cellname['idx']
featurename = pd.read_csv(tissue_dir + 'features.tsv', sep='\t', header=None, index_col=1, names=['gene_ids', 'feature_types'])
adata1.var = featurename
adata1.obs = cellname
adata1.uns["spatial"] = dict()
adata1 = to_spatial(adata1, tissue_dir, library_id='Library_1')
adata1 = adata1[adata1.obs.in_tissue == 1,:]
adata1.var_names_make_unique()
adata1.obs['unnormalized_counts'] = adata1.X.sum(axis=1).A1
sc.pp.normalize_total(adata1, inplace=True)
adata1.obs['normalized_counts'] = adata1.X.sum(axis=1).A1
sc.pp.log1p(adata1)
sc.pp.highly_variable_genes(adata1, flavor="seurat", n_top_genes=2000)
return adata1
⑽ human, mouse 유전자 염기서열 호출 (단, human gene만 입력으로 하면 됨)
from Bio import Entrez
from Bio import SeqIO
from Bio.Blast import NCBIWWW
from Bio.Blast import NCBIXML
import pandas as pd
def human_mouse_gene_sequence(input_gene_name):
# Entrez email setup (required by NCBI)
Entrez.email = "nate9389@gmail.com"
# Function to fetch the sequence using gene ID
def fetch_sequence(gene_id):
handle = Entrez.efetch(db="nucleotide", id=gene_id, rettype="fasta", retmode="text")
record = SeqIO.read(handle, "fasta")
handle.close()
return record.seq
def get_gene_ids(input_gene, file_path="https://blog.kakaocdn.net/dn/cVeqsA/btrS1JMnxyX/HtVhPmqtxdgt7LQlGkeql0/HOM_MouseHumanSequence.csv?attach=1&knm=tfile.csv"):
# Read the CSV file into a DataFrame
df = pd.read_csv(file_path)
# Normalize the input gene name to uppercase to match the 'Symbol' column
input_gene = input_gene.upper()
# Find the row with the human gene symbol
human_row = df[(df['Common Organism Name'] == 'human') & (df['Symbol'].str.upper() == input_gene)]
# If the human gene is not found, return an error message
if human_row.empty:
return "Error: Human gene not found.", None
# Find the corresponding mouse gene using the DB Class Key
db_class_key = human_row['DB Class Key'].values[0]
mouse_row = df[(df['Common Organism Name'] == 'mouse, laboratory') & (df['DB Class Key'] == db_class_key)]
# If the mouse gene is not found, return an error message
if mouse_row.empty:
return None, "Error: Corresponding mouse gene not found."
# Retrieve the gene IDs
human_gene_id = human_row['Nucleotide RefSeq IDs'].values[0].split(',')[0] # Taking the first RefSeq ID if multiple are present
mouse_gene_id = mouse_row['Nucleotide RefSeq IDs'].values[0].split(',')[0] # Taking the first RefSeq ID if multiple are present
return human_gene_id, mouse_gene_id
# Get the human and mouse gene IDs
human_gene_id, mouse_gene_id = get_gene_ids(input_gene_name)
# Fetch the sequences
human_sequence = fetch_sequence(human_gene_id)
mouse_sequence = fetch_sequence(mouse_gene_id)
return human_sequence, mouse_sequence
### Example
human, mouse = human_mouse_gene_sequence("COL1A1")
⑾ image를 Visium anndata obs에 넣는 파이썬 코드
import scanpy as sc
import cv2
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import seaborn as sns
import scipy
tissue_dir1 = './outs/'
adata1 = sc.read_visium(tissue_dir1)
img1 = cv2.imread(tissue_dir1 + 'spatial/tissue_hires_image.png')
img1 = cv2.cvtColor(img1, cv2.COLOR_BGR2RGB)
hires = adata1.uns['spatial']['Parent_Visium_Human_OvarianCancer']['images']['hires']
tissue_hires_scalef = adata1.uns['spatial']['Parent_Visium_Human_OvarianCancer']['scalefactors']['tissue_hires_scalef']
coords = adata1.obsm['spatial'] * tissue_hires_scalef
adata1.obs['img'] = adata1.obs['in_tissue'] # just making a variable
for i in range(adata1.shape[0]):
x_coord = int(np.round(coords[i][0]))
y_coord = int(np.round(coords[i][1]))
# Ensure the coordinates are within the bounds of the image
x_coord = max(0, min(x_coord, hires.shape[1] - 1))
y_coord = max(0, min(y_coord, hires.shape[0] - 1))
# Extract the intensity of the pixel (for simplicity, using the red channel)
intensity = hires[y_coord, x_coord, 0] # Red channel
adata1.obs['img'][i] = intensity
sc.pl.spatial(adata1, color = 'img', img_key=None, spot_size=300)
⑿ Visium ST 데이터를 ann data로 읽어들인 뒤 데이터 QC 작업을 하는 코드
def QC(tissue_dir):
metafile = None
adata1 = sc.read_visium(tissue_dir)
### alternatively ###
# adata1 = sc.read_10x_mtx(tissue_dir)
adata1.var_names_make_unique()
sc.pp.normalize_total(adata1, inplace=True)
sc.pp.log1p(adata1)
# sc.pp.highly_variable_genes(adata1, flavor="seurat", n_top_genes=17189)
adata1.obs['n_counts'] = adata1.X.sum(axis=1).A1
sc.pl.spatial(adata1, img_key="hires", color='n_counts', alpha=0.7, cmap='jet')
return adata1
⒀ sc.pl.spatial 크기 확대하기
fig, ax = plt.subplots(figsize=(10,10))
sc.pl.spatial(adata, color = 'total_counts', ax=ax, show=False)
plt.show()
⒁ sc.pl.spatial의 color bar를 제거하기
import matplotlib.pyplot as plt
import scanpy as sc
sc.pl.spatial(adata, img_key="hires", color='score', alpha=1.0, cmap='viridis', show=False)
fig = plt.gcf()
ax = fig.axes
# Find and remove the colorbar. The colorbar is usually the last axis in the figure.
if len(ax) > 1: # If there's more than one axis (i.e., the colorbar is present)
fig.delaxes(ax[-1]) # Remove the last axis (the colorbar)
plt.show()
⒂ adata를 transpose하기 : gene name과 barcode name 뒤집기
import scanpy as sc
import pandas as pd
# Assuming 'data' is your AnnData object
# Load your AnnData object if it's not already in memory
# data = sc.read_h5ad('/path/to/your/data.h5ad')
# Transpose the data matrix and swap the 'obs' and 'var' DataFrames
adata_transposed = sc.AnnData(X=data.X.T, obs=data.var, var=data.obs)
# If 'obs_names' and 'var_names' need to be retained, you might want to transfer them as well
adata_transposed.obs_names = data.var_names
adata_transposed.var_names = data.obs_names
# Now 'adata_transposed' is the transposed version of ‘data'
⒃ matrix.mtx, barcodes.tsv, features.tsv (or genes.tsv)가 있을 때 h5ad 생성하기 : 단, 세 파일 모두 prefix가 동일하다고 가정
import os
import glob
from scipy.io import mmread
import pandas as pd
import scanpy as sc
# Set the target directory here
target_directory = '/path/to/your/directory'
# Iterate over all .mtx files in the target directory
for mtx_file in glob.glob(os.path.join(target_directory, '*matrix.mtx')):
prefix = mtx_file[:-10] # Remove 'matrix.mtx' to get the prefix
# Construct file names for barcodes and genes
barcodes_file = prefix + 'barcodes.tsv'
features_file = prefix + 'features.tsv'
genes_file = prefix + 'features.tsv' if os.path.exists(prefix + 'features.tsv') else prefix + 'genes.tsv'
# Check if all files exist
if os.path.exists(mtx_file) and os.path.exists(barcodes_file) and os.path.exists(genes_file):
# Load the data
matrix = mmread(mtx_file).T.tocsr() # Transpose to have genes as columns
genes = pd.read_csv(genes_file, header=None, sep='\t')
barcodes = pd.read_csv(barcodes_file, header=None, sep='\t')
# Create an AnnData object
adata = sc.AnnData(X=matrix, obs={'barcodes': barcodes[0].values}, var={'gene_ids': genes[0].values, 'gene_symbols': genes[1].values})
# Output file name
h5ad_file = prefix + '.h5ad'
# Save the AnnData object
adata.write(h5ad_file)
# Delete the original files
os.remove(mtx_file)
os.remove(barcodes_file)
os.remove(genes_file)
print("Conversion complete. Original files have been deleted.")
입력: 2022.05.07 00:43
수정: 2023.10.17 21:16
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