cospar.pl.gene_expression_heatmap¶
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cospar.pl.gene_expression_heatmap(adata, selected_genes=None, selected_fates=None, rename_fates=None, color_bar=True, method='relative', fig_width=6, fig_height=3, horizontal='True', vmin=None, vmax=None, figure_index='', order_map_x=True, order_map_y=True, **kwargs)¶ Plot heatmap of gene expression within given clusters.
- Parameters
- adata :
AnnDataobject - selected_genes : list, optional (default: None)
A list of selected genes.
- selected_fates : list, optional (default: all)
List of cluster ids consistent with adata.obs[‘state_info’]. It allows a nested structure. If so, we merge clusters within each sub-list into a mega-fate cluster.
- method : str, optional (default: ‘relative’)
Method to normalize gene expression. Options: {‘relative’,’zscore’,f’relative_{j}’}. ‘relative’: given coarse-grained gene expression in given clusters, normalize the expression across clusters to be 1; ‘zscore’: given coarse-grained gene expression in given clusters, compute its zscore. f’relative_{j}’: use j-th row for normalization
- rename_fates : list, optional (default: None)
Provide new names in substitution of names in selected_fates. For this to be effective, the new name list needs to have names in exact correspondence to those in the old list.
- color_bar : bool, optional (default: True)
If true, show the color bar.
- fig_width : int, optional (default: 6)
Figure width.
- fig_height : int, optional (default: 3)
Figure height.
- horizontal : bool, optional (default: True)
Figure orientation.
- vmin : float, optional (default: None)
Minimum value to show.
- vmax : float, optional (default: None)
Maximum value to show.
- figure_index
A string for index the figure names.
- order_map_x : bool
Whether to re-order the x coordinate of the matrix or not
- order_map_y : bool
Whether to re-order the y coordinate of the matrix or not
- adata :
- Returns
gene_expression_matrix (np.array)