hv_anndata.DotmapParams¶
- class hv_anndata.DotmapParams(*, expression_cutoff, kdims, marker_genes, max_dot_size, mean_only_expressed, plot_opts, standard_scale, use_raw, vdims, name)¶
Shared parameters.
Parameter Definitions
kdims = List(bounds=(2, 2), default=['marker_line', 'cluster'], label='Kdims')Key dimensions representing cluster and marker line (combined marker cluster name and gene).
vdims = List(bounds=(0, None), default=['gene_id', 'mean_expression', 'percentage', 'marker_cluster_name'], label='Vdims')Value dimensions representing expression metrics and metadata.
marker_genes = ClassSelector(class_=(<class 'dict'>, <class 'list'>), default={}, label='Marker genes')Dictionary or list of marker genes.
expression_cutoff = Number(default=0.0, inclusive_bounds=(True, True), label='Expression cutoff')Cutoff for expression.
max_dot_size = Integer(default=20, inclusive_bounds=(True, True), label='Max dot size')Maximum size of the dots.
standard_scale = Selector(label='Standard scale', names={}, objects=[None, 'var', 'group'])Whether to standardize the dimension between 0 and 1. ‘var’ scales each gene, ‘group’ scales each cell type.
use_raw = Boolean(allow_None=True, label='Use raw')Whether to use .raw attribute of AnnData if present. - None (default): Use .raw if available, otherwise use .X - True: Must use .raw attribute (raises error if not available) - False: Always use .X, ignore .raw even if present In single-cell analysis, .raw typically contains the original count data before normalization, while .X contains processed data (e.g., log-transformed, scaled). Using raw counts is sometimes preferred for visualization to show actual expression levels.
mean_only_expressed = Boolean(default=False, label='Mean only expressed')If True, gene expression is averaged only over expressing cells.
plot_opts = Dict(allow_None=True, class_=<class 'dict'>, label='Plot opts')HoloViews plot options for the Points element.
Attributes