st-spider 0.0.1__tar.gz

st-spider-0.0.1/LICENSE.txt

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+Copyright (c) [year] [fullname]
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

st-spider-0.0.1/PKG-INFO

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+Metadata-Version: 2.1
+Name: st-spider
+Version: 0.0.1
+Summary: A tools to simulate spatial transcriptomics data.
+Home-page: https://github.com/YANG-ERA/Spider/tree/main
+Author: Jiyuan Yang
+Author-email: 599568651@qq.com
+License: MIT
+Description-Content-Type: text/markdown
+License-File: LICENSE.txt
+Requires-Dist: anndata
+Requires-Dist: matplotlib
+Requires-Dist: numba
+Requires-Dist: numpy
+Requires-Dist: pandas
+Requires-Dist: PyQt5
+Requires-Dist: scanpy
+Requires-Dist: scikit_learn
+Requires-Dist: scipy
+Requires-Dist: seaborn
+Requires-Dist: squidpy
+
+
+# Spider: 
+
+Xxx
+
+## Installation
+
+`Spider` is available in [python](https://www.python.org). 
+
+```python
+pip install spider
+```
+
+## Usage
+
+
+
+
+
+## Output files
+
+
+
+
+
+## Citation

st-spider-0.0.1/README.md

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+# Spider: 
+
+Xxx
+
+## Installation
+
+`Spider` is available in [python](https://www.python.org). 
+
+```python
+pip install spider
+```
+
+## Usage
+
+
+
+
+
+## Output files
+
+
+
+
+
+## Citation

st-spider-0.0.1/setup.cfg

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+[egg_info]
+tag_build = 
+tag_date = 0
+

st-spider-0.0.1/setup.py

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+
+import io
+import os
+from setuptools import setup, find_packages
+
+here = os.path.abspath(os.path.dirname(__file__))
+
+try:
+    with io.open(os.path.join(here, 'README.md'), encoding='utf-8') as f:
+        long_description = '\n' + f.read()
+except FileNotFoundError:
+    long_description = DESCRIPTION
+
+
+# Package meta-data.
+NAME = 'st-spider'
+DESCRIPTION = 'A tools to simulate spatial transcriptomics data.'
+EMAIL = '599568651@qq.com'
+URL="https://github.com/YANG-ERA/Spider/tree/main"
+AUTHOR ='Jiyuan Yang'
+VERSION = '0.0.1'
+
+setup(
+    name=NAME,
+    version=VERSION,
+    author=AUTHOR,
+    author_email=EMAIL,
+	license='MIT',
+    description=DESCRIPTION,
+	url=URL,
+    long_description_content_type="text/markdown",
+    long_description=long_description,
+    packages=find_packages(),
+    install_requires=["anndata", "matplotlib", "numba", "numpy",
+                  "pandas", "PyQt5", "scanpy", "scikit_learn",
+                  "scipy", "seaborn", "squidpy"]
+)

st-spider-0.0.1/spider/Annealing.py

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+#import squidpy as sq
+import scanpy as sc
+import anndata as ad
+import numpy as np
+import pandas as pd
+import squidpy as sq
+import matplotlib.pyplot as plt
+import scipy
+import random 
+import matplotlib
+import seaborn as sns
+import math
+#import time
+from scipy.special import softmax
+from scipy.optimize import minimize
+from numpy.random import uniform
+from sklearn.preprocessing import OneHotEncoder
+from sklearn.preprocessing import LabelEncoder
+from .utils import *
+
+def STsim(Num_sample=None,
+          Num_celltype = None,
+          celltype_assignment=None,
+          target_trans = None,
+          T=1000,
+          chain_len=100,
+          error=1e2,
+          tol=2e-2,
+          decay=0.5,
+          onehot_ct=None,
+          nb_count=None,
+          sn=None,
+          swap_num=None,
+          smallsample_max_iter=None,
+          bigsample_max_iter=None):
+    '''
+        smallsample: <10000 and swap_num = 1
+        bigsample: >=10000
+    '''
+
+    error_record = []
+    iter_n = 0
+    print("Refine cell type using Metropolis–Hastings algorithm.")
+    print("Sample num"+":{}".format(Num_sample) )
+
+
+    nb_freq = get_nb_freq(nb_count=nb_count, onehot_ct=onehot_ct)
+    dist_before = sum(scipy.stats.entropy(target_trans, nb_freq))
+
+    if Num_sample <= 10000:
+        swap_num = 1
+        max_iter = smallsample_max_iter
+        criterion3 = True
+        same_errlen = 250
+        while error > tol and iter_n < max_iter and criterion3:
+
+            for i in range(chain_len):
+
+                before_ct_assign, before_onehot_ct, before_nb_count = celltype_assignment.copy(), onehot_ct.copy(), nb_count.copy()
+
+                swap_i, swap_j = swap_ct(
+                    celltype_assignment=celltype_assignment,
+                    Num_celltype=Num_celltype,
+                    swap_num=swap_num)
+
+                celltype_assignment[swap_i[0]], celltype_assignment[
+                    swap_j[0]] = celltype_assignment[
+                        swap_j[0]], celltype_assignment[swap_i[0]]
+                onehot_ct[swap_i[0]], onehot_ct[swap_j[0]] = onehot_ct[
+                    swap_j[0]], onehot_ct[swap_i[0]]
+
+                nb_count = get_swap_nb_count(nb_count=nb_count,
+                                             swap_i=swap_i,
+                                             swap_j=swap_j,
+                                             sn=sn)
+                # nb_count = sn * onehot_ct
+                nb_freq = get_nb_freq(nb_count=nb_count, onehot_ct=onehot_ct)
+
+                dist_after = sum(scipy.stats.entropy(target_trans, nb_freq))
+
+                if 0 > (dist_before - dist_after):
+                    #Reject the swap, so swap back.
+                    p = math.exp((dist_before - dist_after) / T)
+                    r = np.random.uniform(low=0, high=1)
+                    if p < r:
+                        celltype_assignment, nb_count, onehot_ct = before_ct_assign, before_nb_count, before_onehot_ct
+                    else:
+                        dist_before = dist_after
+                else:
+                    dist_before = dist_after
+                iter_n += 1
+        #     print(dist_before - dist_after)
+            T *= decay
+            if iter_n % 100 == 0:
+                error = np.linalg.norm(nb_freq - target_trans)
+                error_record.append(error)
+            if iter_n % 1000 ==0:
+                print("%5d iteration, error %.3f" % (iter_n, error))
+
+            if len(error_record) > same_errlen:
+                if len(set(error_record[-same_errlen:])) == 1:
+                    criterion3 = False
+    else:
+        max_iter = bigsample_max_iter
+        criterion3 = True
+        while error > tol and iter_n < max_iter:
+
+            for i in range(chain_len):
+
+                #dist_before = sum(scipy.stats.entropy(target_trans,nb_freq))
+
+                before_ct_assign, before_onehot_ct, before_nb_count = celltype_assignment.copy(), onehot_ct.copy(), nb_count.copy()
+
+                swap_i, swap_j = swap_ct(
+                    celltype_assignment=celltype_assignment,
+                    Num_celltype=Num_celltype,
+                    swap_num=swap_num)
+
+                celltype_assignment[swap_i[0]], celltype_assignment[
+                    swap_j[0]] = celltype_assignment[
+                        swap_j[0]], celltype_assignment[swap_i[0]]
+                onehot_ct[swap_i[0]], onehot_ct[swap_j[0]] = onehot_ct[
+                    swap_j[0]], onehot_ct[swap_i[0]]
+
+                nb_count = get_swap_nb_count(nb_count=nb_count,
+                                             swap_i=swap_i,
+                                             swap_j=swap_j,
+                                             sn=sn)
+                # nb_count = sn * onehot_ct
+                nb_freq = get_nb_freq(nb_count=nb_count, onehot_ct=onehot_ct)
+
+                dist_after = sum(scipy.stats.entropy(target_trans, nb_freq))
+
+                if 0 > (dist_before - dist_after):
+                    p = math.exp((dist_before - dist_after) / T)
+                    r = np.random.uniform(low=0, high=1)
+                    if p < r:
+                        celltype_assignment, nb_count, onehot_ct = before_ct_assign, before_nb_count, before_onehot_ct
+                    else:
+                        dist_before = dist_after
+                else:
+                    dist_before = dist_after
+                iter_n += 1
+        #     print(dist_before - dist_after)
+            T *= decay
+            if iter_n % 500 == 0:
+                error = np.linalg.norm(nb_freq - target_trans)
+                print("%5d iteration, error %.3f" % (iter_n, error))
+
+    return celltype_assignment

st-spider-0.0.1/spider/MainWidget.py

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+
+from PyQt5.Qt import QWidget, QColor, QPixmap, QIcon, QSize, QCheckBox
+from PyQt5.QtWidgets import QHBoxLayout, QVBoxLayout, QPushButton, QSplitter, \
+    QComboBox, QLabel, QSpinBox, QFileDialog
+
+from paint3.PaintBoard import PaintBoard
+import os
+
+class MainWidget(QWidget):
+
+    def __init__(self, Parent=None):
+
+        super().__init__(Parent)
+
+        self.__InitData()  # initial
+        self.__InitView()
+
+    def __InitData(self):
+
+        self.__paintBoard = PaintBoard(self)
+        self.__colorList = QColor.colorNames()
+
+    def __InitView(self):
+
+        self.setFixedSize(1200, 640)
+        self.setWindowTitle("PaintBoard of PyQt5")
+
+        main_layout = QHBoxLayout(self)
+        main_layout.setSpacing(10)
+
+        main_layout.addWidget(self.__paintBoard)
+
+        sub_layout = QVBoxLayout()
+
+        sub_layout.setContentsMargins(10, 10, 10, 10)
+
+        self.__btn_Clear = QPushButton("Clean")
+        self.__btn_Clear.setParent(self)
+
+        # 将按键按下信号与画板清空函数相关联
+        self.__btn_Clear.clicked.connect(self.__paintBoard.Clear)
+        sub_layout.addWidget(self.__btn_Clear)
+
+        self.__btn_Quit = QPushButton("exit")
+        self.__btn_Quit.setParent(self)
+        self.__btn_Quit.clicked.connect(self.Quit)
+        sub_layout.addWidget(self.__btn_Quit)
+
+        self.__btn_Save = QPushButton("save picture")
+        self.__btn_Save.setParent(self)
+        self.__btn_Save.clicked.connect(self.on_btn_Save_Clicked)
+        sub_layout.addWidget(self.__btn_Save)
+
+        self.__cbtn_Eraser = QCheckBox("use eraser")
+        self.__cbtn_Eraser.setParent(self)
+        self.__cbtn_Eraser.clicked.connect(self.on_cbtn_Eraser_clicked)
+        sub_layout.addWidget(self.__cbtn_Eraser)
+
+        splitter = QSplitter(self)
+        sub_layout.addWidget(splitter)
+
+        self.__label_penThickness = QLabel(self)
+        self.__label_penThickness.setText("Pen thickness")
+        self.__label_penThickness.setFixedHeight(20)
+        sub_layout.addWidget(self.__label_penThickness)
+
+        self.__spinBox_penThickness = QSpinBox(self)
+        self.__spinBox_penThickness.setMaximum(20)
+        self.__spinBox_penThickness.setMinimum(2)
+        self.__spinBox_penThickness.setValue(10)
+        self.__spinBox_penThickness.setSingleStep(2)
+        self.__spinBox_penThickness.valueChanged.connect(
+            self.on_PenThicknessChange)
+        sub_layout.addWidget(self.__spinBox_penThickness)
+
+        self.__label_penColor = QLabel(self)
+        self.__label_penColor.setText("Pen color")
+        self.__label_penColor.setFixedHeight(20)
+        sub_layout.addWidget(self.__label_penColor)
+
+        self.__comboBox_penColor = QComboBox(self)
+        self.__fillColorList(self.__comboBox_penColor)
+        self.__comboBox_penColor.currentIndexChanged.connect(
+            self.on_PenColorChange)
+        sub_layout.addWidget(self.__comboBox_penColor)
+
+        main_layout.addLayout(sub_layout)
+
+    def __fillColorList(self, comboBox):
+
+        index_black = 0
+        index = 0
+        for color in self.__colorList:
+            if color == "black":
+                index_black = index
+            index += 1
+            pix = QPixmap(70, 20)
+            pix.fill(QColor(color))
+            comboBox.addItem(QIcon(pix), None)
+            comboBox.setIconSize(QSize(70, 20))
+            comboBox.setSizeAdjustPolicy(QComboBox.AdjustToContents)
+
+        comboBox.setCurrentIndex(index_black)
+
+    def on_PenColorChange(self):
+        color_index = self.__comboBox_penColor.currentIndex()
+        color_str = self.__colorList[color_index]
+        self.__paintBoard.ChangePenColor(color_str)
+
+    def on_PenThicknessChange(self):
+        penThickness = self.__spinBox_penThickness.value()
+        self.__paintBoard.ChangePenThickness(penThickness)
+
+    def on_btn_Save_Clicked(self):
+        # savePath = QFileDialog.getSaveFileName(self, 'Save Your Paint', '.\\', '*.png')
+        # print(savePath)
+        # if savePath[0] == "":
+        #     print("Save cancel")
+        #     return
+        #savePath = "C:\\Users\\quyang\\paint2\\test.png"
+        ####
+        image = self.__paintBoard.GetContentAsQImage()
+        #image.save(savePath)
+
+        image.save(os.getcwd()+"/test.jpg")
+
+    def on_cbtn_Eraser_clicked(self):
+        if self.__cbtn_Eraser.isChecked():
+            self.__paintBoard.EraserMode = True
+        else:
+            self.__paintBoard.EraserMode = False
+
+    def Quit(self):
+        self.close()

st-spider-0.0.1/spider/PaintBoard.py

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+#https://blog.csdn.net/CreatorGG/article/details/81542837?spm=1001.2101.3001.6650.14&utm_medium=distribute.pc_relevant.none-task-blog-2%7Edefault%7EBlogCommendFromBaidu%7ERate-14-81542837-blog-118923269.pc_relevant_multi_platform_featuressortv2dupreplace&depth_1-utm_source=distribute.pc_relevant.none-task-blog-2%7Edefault%7EBlogCommendFromBaidu%7ERate-14-81542837-blog-118923269.pc_relevant_multi_platform_featuressortv2dupreplace&utm_relevant_index=20
+'''
+Created on 2018年8月9日
+
+@author: Freedom
+'''
+from PyQt5.QtWidgets import QWidget
+from PyQt5.Qt import QPixmap, QPainter, QPoint, QPaintEvent, QMouseEvent, QPen, \
+    QColor, QSize
+from PyQt5.QtCore import Qt
+
+
+class PaintBoard(QWidget):
+
+    def __init__(self, Parent=None):
+        '''
+        Constructor
+        '''
+        super().__init__(Parent)
+
+        self.__InitData()
+        self.__InitView()
+
+    def __InitData(self):
+
+        self.__size = QSize(1000, 600)
+
+        self.__board = QPixmap(self.__size)
+        self.__board.fill(Qt.white)
+
+        self.__IsEmpty = True
+        self.EraserMode = False
+
+        self.__lastPos = QPoint(0, 0)
+        self.__currentPos = QPoint(0, 0)
+
+        self.__painter = QPainter()
+
+        self.__thickness = 10
+        self.__penColor = QColor("black")
+        self.__colorList = QColor.colorNames()
+
+    def __InitView(self):
+        self.setFixedSize(self.__size)
+
+    def Clear(self):
+        self.__board.fill(Qt.white)
+        self.update()
+        self.__IsEmpty = True
+
+    def ChangePenColor(self, color="black"):
+        self.__penColor = QColor(color)
+
+    def ChangePenThickness(self, thickness=10):
+        self.__thickness = thickness
+
+    def IsEmpty(self):
+        return self.__IsEmpty
+
+    def GetContentAsQImage(self):
+        image = self.__board.toImage()
+        return image
+
+    def paintEvent(self, paintEvent):
+        self.__painter.begin(self)
+        self.__painter.drawPixmap(0, 0, self.__board)
+        self.__painter.end()
+
+    def mousePressEvent(self, mouseEvent):
+        self.__currentPos = mouseEvent.pos()
+        self.__lastPos = self.__currentPos
+
+    def mouseMoveEvent(self, mouseEvent):
+        self.__currentPos = mouseEvent.pos()
+        self.__painter.begin(self.__board)
+
+        if self.EraserMode == False:
+            self.__painter.setPen(QPen(self.__penColor, self.__thickness))  # 设置画笔颜色，粗细
+        else:
+            self.__painter.setPen(QPen(Qt.white, 10))
+
+        self.__painter.drawLine(self.__lastPos, self.__currentPos)
+        self.__painter.end()
+        self.__lastPos = self.__currentPos
+
+        self.update()
+
+    def mouseReleaseEvent(self, mouseEvent):
+        self.__IsEmpty = False 
+
+
+

st-spider-0.0.1/spider/__init__.py

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+from  .run_scsim import *
+from .scsim import *
+from .sim_expr import *
+from .simulate_10X import *