multivelovae.scatter_plot

multivelovae.scatter_plot(adata, adata_atac, genes, key='vae', by='us', modalities=None, modalities_pred=None, color_by=None, n_cols=5, axis_on=True, frame_on=True, show_pred=True, show_pred_only=False, batch_correction=False, title_more_info=False, velocity_arrows=False, downsample=1, figsize=None, pointsize=2, fontsize=11, cmap='coolwarm', view_3d_elev=None, view_3d_azim=None, full_name=False)

Gene scatter plot.

This function plots phase portraits of the specified plane.

Args:

adata anndata.AnnData:

Anndata result after VAE inference.

adata_atac anndata.AnnData:

ATAC Anndata object.

genes [str, list of str]:

List of genes to plot.

key (str, optional):

Key to find VAE variables. Defaults to vae.

by (str):

Plot unspliced-spliced plane if us. Plot chromatin-unspliced plane if cu. Plot 3D phase portraits if cus. Defaults to ‘us’.

modalities (list, optional):

List of modalities in adata.layers to plot. Defaults to None.

modalities_pred (list, optional):

List of predicted modalities in adata.layers to plot. Defaults to None.

color_by: (str, optional):

Color used for the plots. Defaults to None.

n_cols (int):

Number of columns to plot. Defaults to 5.

axis_on (bool):

Whether to show axis labels. Defaults to True.

frame_on (bool):

Whether to show plot frames. Defaults to True.

show_pred (bool):

Whether to show prediction. Defaults to True.

show_pred_only (bool):

Whether to show prediction only. Defaults to False.

batch_correction (bool):

Whether the output was generated with batch correction. Defaults to False.

title_more_info (bool):

Whether to show likelihood for the gene in title. Defaults to False.

velocity_arrows (bool):

Whether to show velocity arrows of cells on the phase portraits. Defaults to False.

downsample (int):

How much to downsample the cells. The remaining number will be 1/downsample of original. Defaults to 1.

figsize (tuple):

Total figure size. Defaults to None.

pointsize (float):

Point size for scatter plots. Defaults to 2.

fontsize (int):

Font size for title. Defaults to 11.

cmap: (str)

Color map for continuous color key. Defaults to ‘coolwarm’.

view_3d_elev (float):

Matplotlib 3D plot elev argument. elev=90 is the same as U-S plane, and elev=0 is the same as C-U plane. Defaults to None.

view_3d_azim (float):

Matplotlib 3D plot azim argument. azim=270 is the same as U-S plane, and azim=0 is the same as C-U plane. Defaults to None.

full_name (bool):

Show full names for chromatin, unspliced, and spliced rather than using abbreviated terms c, u, and s. Defaults to False.