gefpy.cgef_adjust_cy

Provides access to the cgef_adjust interface.

class cgef_adjust_cy.CgefAdjust

get_cell_data(self, bgef, cgef)

Get raw cell data from cgef and bgef file.

Parameters

• bgef – the bgef file path

• cgef – the cgef file path

Returns

(genelist, vec_cell)

write_cgef_adjustdata(self, path, celldata, dnbdata)

write the adjust cell data to cgef

Parameters

• path – set the Output path

• celldata – input the cell data

• dandata – input the dandata

create_Region_Bgef(self, inpath, outpath, pos)

generate spatial bin gef file by lasso region datas

Parameters

• inpath – the bgef file path

• outpath – set the Output path

• pos – lasso region datas

create_Region_Cgef(self, inpath, outpath, pos)

generate cell bin gef file by lasso region datas

Parameters

• inpath – the cgef file path

• outpath – set the Output path

• pos – lasso region datas

get_regiondata_frombgef(self, inpath, bin, thcnt, pos)

Get gene info from spatial bin gef file by lasso region datas

Parameters

• inpath – the bgef file path

• bin – set bin size

• thcnt – thread counts

• pos – lasso region datas

Returns vecdata

gene info{genecnt,midcnt,x,y} in region

get_regiondata_fromcgef(self, input_path, pos)

Get cell statistical info from cell bin gef file by lasso region datas

Parameters

• input_path – the cgef file path

• pos – lasso region datas

Returns vecdata

statistical info{cell_count,total_area,average_gene_count,average_exp_count,average_dnb_count,average_area,median_gene_count,median_exp_count,median_dnb_count,median_area} in region