pegasus.heatmap

pegasus.heatmap(data, attrs, groupby, matkey=None, on_average=True, switch_axes=False, attrs_cluster=False, attrs_dendrogram=True, groupby_cluster=True, groupby_dendrogram=True, attrs_labelsize=10.0, groupby_labelsize=10.0, 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) – 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.

  • 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.

  • on_average (bool, optional, default: True) – If True, plot cluster average gene expression (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.

  • 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.

  • attrs_labelsize (float, optional, default: 10.0) – Fontsize for labels of attrs.

  • groupby_labelsize (float, optional, default: 10.0) – Fontsize for labels of data.obs[‘groupby’].

  • 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) –

Returns

A matplotlib.figure.Figure object containing the dot plot if return_fig == True

Return type

Figure object

Examples

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