plot_RGB

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

plot_RGB function

<dl> <dt>position</dt>
<dd>a coordinates matrix with two columns: x-coordinate and y-coordinate.</dd> <dt>embed_3d</dt>
<dd>a embedding matrix with three columns: x, y and z embeddings.</dd> <dt>pointsize</dt>
<dd>the size of point in the scatter plot.</dd> <dt>textsize</dt>
<dd>the text size in the plot.</dd></dl>

Arguments

Author

Spatial RGB heatmap — plot_RGB

<dl>

 <dt>position</dt>
<dd>a coordinates matrix with two columns: x-coordinate and y-coordinate.</dd>

 <dt>embed_3d</dt>
<dd>a embedding matrix with three columns: x, y and z embeddings.</dd>

 <dt>pointsize</dt>
<dd>the size of point in the scatter plot.</dd>

 <dt>textsize</dt>
<dd>the text size in the plot.</dd>

</dl>

plot_RGB: Spatial RGB heatmap

Description

Usage

Value

Arguments

Author

Details

See Also