pegasus.heatmap

pegasus.heatmap(data, attrs, groupby=None, matkey=None, gene_zscore=True, on_average=True, switch_axes=False, attrs_cluster=False, attrs_dendrogram=True, attrs_method='ward', attrs_optimal_ordering=True, xlabel_size=10.0, ylabel_size=10.0, legend_fontsize=10.0, xlabel_rotation=90.0, ylabel_rotation=0.0, groupby_cluster=True, groupby_dendrogram=True, groupby_method='ward', groupby_optimal_ordering=True, groupby_precomputed_linkage=None, show_sample_name=None, cbar_labelsize=10.0, panel_size=(10, 10), return_fig=False, dpi=300.0, **kwargs)[source]

Generate a heatmap.

Parameters

  • data (AnnData or MultimodalData or UnimodalData object) – Single-cell expression data.

  • attrs (str or List[str]) – Cell attributes or features to plot. Cell attributes must exist in data.obs and must be numeric. Features must exist in data.var. By default, attrs are plotted as columns.

  • groupby (str, optional, default: None) – A categorical variable in data.obs that is used to categorize the cells, e.g. Clusters. By default, data.obs[‘groupby’] is plotted as rows. If None, use data.obs_names instead.

  • matkey (str, optional, default: None) – If matkey is set, select matrix with matkey as keyword in the current modality. Only works for MultimodalData or UnimodalData objects.

  • gene_zscore (bool, optional, default: True) – If True, compute and then plot z scores for gene expression.

  • on_average (bool, optional, default: True) – If True, plot cluster average gene expression or z score (i.e. show a Matrixplot); otherwise, plot a general heatmap.

  • switch_axes (bool, optional, default: False) – By default, X axis is for attributes, and Y axis for clusters. If this parameter is True, switch the axes. Moreover, with on_average being False, if switch_axes is False, row_cluster is enforced to be False; if switch_axes is True, col_cluster is enforced to be False.

  • attrs_cluster (bool, optional, default: False) – Cluster attributes and generate a attribute-wise dendrogram.

  • attrs_dendrogram (bool, optional, default: True) – Only matters if attrs_cluster is True. Show the dendrogram if this option is True.

  • attrs_method (str, optional, default: ward) – Linkage method for attrs, choosing from single, complete, average, weighted, centroid, median and ward.

  • attrs_optimal_ordering (bool, optional, default: True) – Parameter for scipy.cluster.hierarchy.linkage. If True, the attrs linkage matrix will be reordered so that the distance between successive leaves is minima.

  • xlabel_size (float, optional, default: 10.0) – Fontsize for x-axis labels.

  • ylabel_size (float, optional, default: 10.0) – Fontsize for y-axis labels.

  • legend_fontsize (float, optional, default: 10.0) – Fontsize for legend labels.

  • xlabel_rotation (float, optional, default: 90.0) – Rotation of x-axis labels.

  • ylabel_rotation (float, optional, default: 0.0) – Rotation of y-axis labels.

  • groupby_cluster (bool, optional, default: True) – Cluster data.obs[‘groupby’] and generate a cluster-wise dendrogram.

  • groupby_dendrogram (bool, optional, default: True) – Only matters if groupby_cluster is True. Show the dendrogram if this option is True.

  • groupby_method (str, optional, default: ward) – Linkage method for groupby, choosing from single, complete, average, weighted, centroid, median and ward.

  • groupby_optimal_ordering (bool, optional, default: True) – Parameter for scipy.cluster.hierarchy.linkage. If True, the groupby linkage matrix will be reordered so that the distance between successive leaves is minima.

  • groupby_precomputed_linkage (np.array, optional, default: None) – Pass a precomputed linkage.

  • show_sample_name (bool, optional, default: None) – If show sample names as tick labels. If None, show_sample_name == True if groupby == None and otherwise show_sample_name == False.

  • cbar_labelsize (float, optional, default: 10.0) – Fontsize of the color bar.

  • panel_size (Tuple[float, float], optional, default: (10, 10)) – Overall size of the heatmap in (width, height) form.

  • return_fig (bool, optional, default: False) – Return a Figure object if True; return None otherwise.

  • dpi (float, optional, default: 300.0) – The resolution in dots per inch.

  • kwargs – Are passed to seaborn.heatmap.

  • documentation (.. _colormap) –

Return type

Optional[Figure]

Returns

  • Figure object – A matplotlib.figure.Figure object containing the heatmap if return_fig == True; Otherwise, A seaborn.matrix.ClusterGrid object is returned.

Examples

>>> pg.heatmap(data, attrs=['CD14', 'TRAC', 'CD34'], groupby='leiden_labels')