def formCellTypeTree(n, cells, cellTypeParents, cellTypeNumCells, cellTypeConstProps, transcriptionFactors, cellTypeMeans): cellTypeTree = Tree() parentCellType = -1 projInit = np.ones(shape=n) constInit = np.zeros(shape=n) cellTypeMember = [] cellTypeChildMember = list(range(cells)) cellTypeMean = 0 numCellTypes = len(cellTypeParents) projMatrix = np.zeros(shape = (numCellTypes, n)) constMatrix = np.zeros(shape = (numCellTypes, n)) headNode = cellTypeTree.add_head(parentCellType, cellTypeMember, constInit, projInit, cellTypeMean) headNode.setChildCellTypeMembers(cellTypeChildMember) numCellTypes = len(cellTypeParents) cellTypeMembers = [[] for i in range(numCellTypes)] cellNumPool = range(cells) for cellType in range(numCellTypes): numCells = cellTypeNumCells[cellType] cellTypeIndices = random.sample(cellNumPool, numCells) cellTypeMembers[cellType] = cellTypeIndices cellNumPool = list(set(cellNumPool) - set(cellTypeIndices)) addTreeChildren(n, cellTypeTree, cellTypeParents, cellTypeMembers, cellTypeConstProps, projInit, constInit, projMatrix, constMatrix, cellTypeMeans, parentCellType, transcriptionFactors) #maxCellType = int(max(cellTypeParents)) #Highest cell type number corresponds to the highest cell type for node in cellTypeTree.traverse(-1): for field in node: print(field) return cellTypeTree, projMatrix, constMatrix
def formCellTypeTree(n, cells, cellTypeParents, cellTypeNumCells,
cellTypeConstProps, transcriptionFactors, cellTypeMeans):
"""
Parameters
----------
n : int
number of genes
cells : int
number of cells
cellTypeParents :
the value of index `i` is the parent of cell type `i`
cellTypeNumCells :
the value of index `i` is the number of cells of type `i` to end up with
cellTypeConstProps :
proportion of transcription factors to set constant indexed by cell type
transcriptionFactors :
list of genes with positive outdegree
Returns
-------
cellTypeTree :
a tree representation of cell development
projMatrix :
collection of 0/1 projection vectors, one for each cell type
constMatrix :
collection of constant vectors, one for each cell type
"""
cellTypeTree = Tree()
parentCellType = -1
projInit = np.ones(shape=n)
constInit = np.zeros(shape=n)
cellTypeMember = []
cellTypeChildMember = list(range(cells))
cellTypeMean = 0
numCellTypes = len(cellTypeParents)
projMatrix = np.zeros(shape=(numCellTypes, n))
constMatrix = np.zeros(shape=(numCellTypes, n))
headNode = cellTypeTree.add_head(parentCellType, cellTypeMember, constInit,
projInit, cellTypeMean)
headNode.setChildCellTypeMembers(cellTypeChildMember)
numCellTypes = len(cellTypeParents)
cellTypeMembers = [[] for i in range(numCellTypes)]
cellNumPool = range(cells)
for cellType in range(numCellTypes):
numCells = cellTypeNumCells[cellType]
cellTypeIndices = random.sample(cellNumPool, numCells)
cellTypeMembers[cellType] = cellTypeIndices
cellNumPool = list(set(cellNumPool) - set(cellTypeIndices))
addTreeChildren(n, cellTypeTree, cellTypeParents, cellTypeMembers,
cellTypeConstProps, projInit, constInit, projMatrix,
constMatrix, cellTypeMeans, parentCellType,
transcriptionFactors)
#maxCellType = int(max(cellTypeParents)) #Highest cell type number corresponds to the highest cell type
# for node in cellTypeTree.traverse(-1):
# for field in node:
# print(field)
return cellTypeTree, projMatrix, constMatrix