multivelo.scatter_plot

multivelo.scatter_plot(adata, genes, by='us', color_by='state', n_cols=5, axis_on=True, frame_on=True, show_anchors=True, show_switches=True, show_all_anchors=False, title_more_info=False, velocity_arrows=False, downsample=1, figsize=None, pointsize=2, markersize=5, linewidth=2, 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.

Parameters:

  • adata (AnnData) – Anndata result from dynamics recovery.

  • genes (str, list of str) – List of genes to plot.

  • by (str (default: us)) – Plot unspliced-spliced plane if us. Plot chromatin-unspliced plane if cu. Plot 3D phase portraits if cus.

  • color_by (str (default: state)) – Color by the four potential states if state. Other common values are leiden, louvain, celltype, etc. If not state, the color field must be present in .uns, which can be pre-computed with scanpy.pl.scatter. For state, red, orange, green, and blue represent state 1, 2, 3, and 4, respectively. When by==’us’, color_by can also be c, which displays the log accessibility on U-S phase portraits.

  • n_cols (int (default: 5)) – Number of columns to plot on each row.

  • axis_on (bool (default: True)) – Whether to show axis labels.

  • frame_on (bool (default: True)) – Whether to show plot frames.

  • show_anchors (bool (default: True)) – Whether to display anchors.

  • show_switches (bool (default: True)) – Whether to show switch times. The three switch times and the end of trajectory are indicated by circle, cross, dismond, and star, respectively.

  • show_all_anchors (bool (default: False)) – Whether to display full range of (predicted) anchors even for repression-only genes.

  • title_more_info (bool (default: False)) – Whether to display model, direction, and likelihood information for the gene in title.

  • velocity_arrows (bool (default: False)) – Whether to show velocity arrows of cells on the phase portraits.

  • downsample (int (default: 1)) – How much to downsample the cells. The remaining number will be 1/downsample of original.

  • figsize (tuple (default: None)) – Total figure size.

  • pointsize (float (default: 2)) – Point size for scatter plots.

  • markersize (float (default: 5)) – Point size for switch time points.

  • linewidth (float (default: 2)) – Line width for connected anchors.

  • cmap (str (default: coolwarm)) – Color map for log accessibilities or other continuous color keys when plotting on U-S plane.

  • view_3d_elev (float (default: None)) – Matplotlib 3D plot elev argument. elev=90 is the same as U-S plane, and elev=0 is the same as C-U plane.

  • view_3d_azim (float (default: None)) – Matplotlib 3D plot azim argument. azim=270 is the same as U-S plane, and azim=0 is the same as C-U plane.

  • full_name (bool (default: False)) – Show full names for chromatin, unspliced, and spliced rather than using abbreviated terms c, u, and s.