Cnv

missionbio.mosaic.cnv.Cnv

class Cnv(*args, **kwargs)

Container for CNV data.

Inherits most methods from _Assay. See that for the documentation on other methods and visualizations.

Filtering

filter_amplicons([completeness, read_depth])

Remove amplicons with missing information.

Algorithms

compute_ploidy(diploid_cells[, ...])	Computes the ploidy of the cells
get_gene_names([max_workers, species])	Fetch gene names from Ensembl for all the amplicons.
name_id_by_pos()	Renames the ids using the chromosome and position
normalize_reads()	Normalize the read counts.
model_amplicons()	Fit the CNV amplicon model and return the LikelihoodMethod object.

CNV specific visualizations

plot_ploidy(cluster[, features, collapse])	Plots the ploidy of the cluster
amp_uniformity([title])	Plot amplicon uniformity.
cell_uniformity([title])	Plot cell uniformity.
update_coloraxis(fig, layer[, coloraxis, ...])	Sets the colorscale for DNA.

Extended methods

heatmap(attribute[, splitby, features, ...])	Extends heatmap()
signaturemap(attribute[, kind, nan_value, ...])	Extends signaturemap()

Parameters:

argslist

To be passed to the _Assay class.

kwargsdict

To be passed to the _Assay class.