gcell.cell.celltype.GETHydraCellType#
- class gcell.cell.celltype.GETHydraCellType(celltype, zarr_path, prediction_target='exp')[source]#
Cell type class optimized for hydra model analysis.
This class extends the base Celltype class with functionality specific to the hydra model architecture, including zarr-based data storage and efficient processing of large datasets.
Attributes
This method retrieves gene data by motif.
Methods
from_config(cfg[, celltype, zarr_path, ...])Create GETHydraCellType instance from configuration.
gene_jacobian_summary(gene[, axis, ...])Summarizes the Jacobian for a given gene.
get_gene_accessibility(gene_name)Get the accessibility of a gene.
get_gene_annot(gene_name)Get the gene annotation of a gene.
get_gene_by_motif([overwrite])Calculate gene by motif data for hydra-based cell-type.
get_gene_chromosome(gene_name)Get the chromosome of a gene.
get_gene_idx(gene_name)Get all indices for a given gene name.
get_gene_jacobian(gene_name[, ...])Get jacobians for all TSS of a gene.
get_gene_jacobian_region_norm(gene_name[, ...])Get jacobians L2 norm per region for all TSS of a gene.
get_gene_jacobian_summary(gene_name[, axis])Get the jacobian summary of a gene.
get_gene_obs(gene_name)Get the observed value of a gene.
get_gene_pred(gene_name)Get the prediction of a gene.
get_gene_strand(gene_name)Get strand information for a gene.
get_gene_tss(gene_name)Get the TSS objects of a gene.
get_gene_tss_start(gene_name)Get the start position of a gene.
get_genes_exp(genes)Get the expression of a list of genes.
get_highest_exp_genes(genes)This code takes in a list of genes and returns the gene with the highest expression value.
get_input_data([peak_id, focus, start, end])Get input data from self.input_all using a slice
get_powerlaw_at_distance(distances[, ...])Get the powerlaw trained on k562 Hi-C data at a given distance.
get_tf_exp_mean(motif, m)Calculate the mean expression of transcription factors (TFs) for a given motif and cluster.
get_tf_exp_str(motif, m)This method generates a formatted string of gene names and their corresponding predicted expression values.
get_tf_pathway(tf[, gp, quantile_cutoff, ...])This function retrieves the pathway for a given transcription factor (tf) using g:Profiler.
get_tss_idx(gene_name)Given a gene name, get the TSS index in the peak annotation.
get_tss_jacobian(jacob, tss[, multiply_input])Get the jacobian of a TSS.
Override parent method - not needed for GETHydraCellType.
plot_gene_motifs(gene[, motif, overwrite, n])Plot top N motifs for a gene.
plot_gene_regions(gene[, plotly])plotly_motif_subnet(motif, m[, type, threshold])Plots a subnet of motifs.