Method get_gene

scTDA/main.py:1734–1751

Returns a dictionary that asigns to each node id the average value of the column 'genin' in the raw table. 'genin' can be also a list of columns, on which case the average of all columns. The output is normalized such that the sum over all nodes is equal to 1. It also provid

(self, genin, ignore_log=False, con=True)

            return [None, None]

    def get_gene(self, genin, ignore_log=False, con=True):
        """
        Returns a dictionary that asigns to each node id the average value of the column 'genin' in the raw table.
        'genin' can be also a list of columns, on which case the average of all columns. The output is normalized
        such that the sum over all nodes is equal to 1. It also provides as an output the normalization factor, to
        convert the dictionary to log_2(1+TPM) units (or TPM units). When 'ignore_log' is True it treat entries as
        being in natural scale, even if self.log2 is True (used internally). When 'con' is False, it uses all
        nodes, not only the ones in the first connected component of the topological representation (used internally).
        Argument 'genin' may also be equal to the special keyword '_dist_root', on which case it returns the graph
        distance funtion to the root node. It can be also equal to 'timepoint_xxx', on which case it returns a
        dictionary with the fraction of cells belonging to timepoint xxx in each node.
        """
        if genin == '_dist_root':
            return self.get_distroot(self.root), 1.0
        elif genin is not None and 'timepoint_' in genin:
            return self.count_gene(self.rootlane, float(genin[genin.index('_')+1:]))
        else:
            return UnrootedGraph.get_gene(self, genin, ignore_log, con)

    def draw_expr_timeline(self, genin, ignore_log=False, path=False, save='', axis=[], smooth=False):
        """