doHeatmap

Plot heatmap for a Seurat object with expressioin data.

An efficient data integration method is provided for multiple spatial transcriptomics data with non-cluster-relevant effects such as the complex batch effects. It unifies spatial factor analysis simultaneously with spatial clustering and embedding alignment, requiring only partially shared cell/domain clusters across datasets. More details can be referred to Wei Liu, et al. (2023) <doi:10.1038/s41467-023-35947-w>.

Wei Liu

PRECAST

Embedding and Clustering with Alignment for Spatial Datasets

Yi Yang

Jin Liu

doHeatmap function

<dl> <dt>seu</dt>
<dd>an object named "Seurat". The object of class "Seurat" must include slot "scale.data".</dd> <dt>features</dt>
<dd>an optional string vector, the features to be plotted.</dd> <dt>cell_label</dt>
<dd>an optional string, the name of legend.</dd> <dt>grp_label</dt>
<dd>an optional logical value, whether display the group names.</dd> <dt>pt_size</dt>
<dd>the point size used in the plot</dd> <dt>grp_color</dt>
<dd>the colors to use for the group color bar.</dd> <dt>...</dt>
<dd>Other paramters passed to DoHeatmap.</dd></dl>

Arguments

Author

Heatmap for spots-by-feature matrix — doHeatmap

<dl>

 <dt>seu</dt>
<dd>an object named "Seurat". The object of class "Seurat" must include slot "scale.data".</dd>

 <dt>features</dt>
<dd>an optional string vector, the features to be plotted.</dd>

 <dt>cell_label</dt>
<dd>an optional string, the name of legend.</dd>

 <dt>grp_label</dt>
<dd>an optional logical value, whether display the group names.</dd>

 <dt>pt_size</dt>
<dd>the point size used in the plot</dd>

 <dt>grp_color</dt>
<dd>the colors to use for the group color bar.</dd>

 <dt>...</dt>
<dd>Other paramters passed to DoHeatmap.</dd>

</dl>

doHeatmap: Heatmap for spots-by-feature matrix

Description

Usage

Value

Arguments

Author

Details

See Also

Examples