gefpy.cgef_reader_cy
Provides access to the cgef_reader interface.
- class cgef_reader_cy.CgefR(filepath)
- get_expression_num(self)
Get the number of expression.
- get_cell_num(self)
Get the number of cell.
- get_gene_num(self)
Get the number of gene.
- get_gene_names(self)
Get a list of gene names. The type of gene name is 32 chars.
- get_cell_names(self)
Get an array of cell ids. Each cell id is (cell.x <<32 | cell.y)
- get_cells(self)
Get cells, each cell include (id, x, y, offset, geneCount, expCount, dnbCount, area, cellTypeID, clusterID)
- get_genes(self)
Get genes, each gene include(geneName, offset, cellCount, expCount, maxMIDcount)
- get_cellid_and_count(self)
Get the count of each cell in each gene.
- Returns
(cell_id, count)
- get_geneid_and_count(self)
Get the count of each gene in each cell.
- Returns
(gene_id, count)
- get_cellborders(self)
Gets cell borders.
- Returns
borders_list
- get_filtered_data(self, region, genelist)
Get the filtered data from cgef by region or gene.
- Parameters
region – rect region(minx,maxx,miny,maxy)
genelist – gene name list
uniq_cell is list that save all cell, each cell val (exp.x<<32 | exp.y).
gene_names is a list of gene names.
count is a list that save the midcnt of each expression.
cell_index is a list that save the cell idx of each expression.
gene_index is a list that records the gene serial number corresponding to each exp.
- Returns
(uniq_cell, gene_names, count, cell_index, gene_index)