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
orMultimodalData
orUnimodalData
object) – Single-cell expression data.attrs (
str
orList[str]
) – Cell attributes or features to plot. Cell attributes must exist indata.obs
and must be numeric. Features must exist indata.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
) – IfTrue
, 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 isTrue
, switch the axes. Moreover, withon_average
beingFalse
, ifswitch_axes
isFalse
,row_cluster
is enforced to beFalse
; ifswitch_axes
isTrue
,col_cluster
is enforced to beFalse
.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 aFigure
object ifTrue
; returnNone
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 ifreturn_fig == True
- Return type
Figure
object
Examples
>>> pg.heatmap(data, genes=['CD14', 'TRAC', 'CD34'], groupby='louvain_labels')