Plotting with scanpy

plotting.dotplot(adata, markers, cluster_header, *, dendrogram=True, save=False, output_folder='', outputfilename_suffix='', **kwargs)

Generating scanpy dotplot of adata with input marker list.

Parameters:

adata: AnnData

Annotated data matrix.

markers: list | dict

List of markers to show in dotplot. Dictionary of markers per cell type to group by.

cluster_header: str

Column in adata.obs storing cell annotation.

dendrogram: bool | list (default: True)

Whether to use dendrogram from adata.uns[“dendrogram_{cluster_header}”]. If list, dendrogram order.

save: bool | str (default: False)

Whether to save plot. If string, choose the type of file to save as (“png”, “jpeg”, “webp”, “svg”, “pdf”).

output_folder: str (default: “.”)

Output folder. Created if doesn’t exist.

outputfilename_suffix: str (default: “”)

Prefix for all output files.

kwargs: dictionary (default: None)

Additional parameters to pass to sc.pl.dotplot.

plotting.stackedviolin(adata, markers, cluster_header, *, dendrogram=True, save=False, output_folder='', outputfilename_suffix='', **kwargs)

Generating scanpy stacked_violin of adata with input marker list.

Parameters:

adata: AnnData

Annotated data matrix.

markers: list/dict

List of markers to show in dotplot. Dictionary of markers per cell type to group by.

cluster_header: str

Key in adata.obs storing cell type.

dendrogram: bool/list (default: True)

Whether to use dendrogram from adata.uns[“dendrogram_{cluster_header}”]. Dendrogram order.

save: bool, str (default: False)

Whether to save plot. Set as option for type of image to save (“html”, “svg”, “png”, etc)

output_folder: str (default: “.”)

Output folder. Created if doesn’t exist.

outputfilename_suffix: str (default: “”)

Prefix for all output files.

kwargs: dictionary (default: None)

Additional parameters to pass to sc.pl.stacked_violin.

plotting.matrixplot(adata, markers, cluster_header, *, dendrogram=True, save=False, output_folder='', outputfilename_suffix='', **kwargs)

Generating scanpy matrixplot of adata from markers.

Parameters:

adata: AnnData

Annotated data matrix.

markers: list/dict

List of markers to show in dotplot. Dictionary of markers per cell type to group by.

cluster_header: str

Key in adata.obs storing cell type.

dendrogram: bool/list (default: True)

Whether to use dendrogram from adata.uns[“dendrogram_{cluster_header}”]. Dendrogram order.

save: bool, str (default: False)

Whether to save plot. Set as option for type of image to save (“html”, “svg”, “png”, etc)

output_folder: str (default: “.”)

Output folder. Created if doesn’t exist.

outputfilename_suffix: str (default: “”)

Prefix for all output files.

kwargs: dictionary (default: None)

Additional parameters to pass to sc.pl.matrixplot.