Visualize vector field on embedding. Adapted from scvelo.
Usage
plot_vector_field(
seurat_obj,
zs_key = "X_zs",
vf_key = "X_VF",
embedding_key = "umap",
reverse = FALSE,
n_neigh = 20,
t_key = NULL,
var_transform = FALSE,
scale = 10,
self_transition = FALSE,
smooth = 0.5,
density = 1,
grid = FALSE,
stream = TRUE,
stream_density = 2,
stream_color = "black",
stream_linewidth = 0.5,
stream_arrowsize = 0.3,
grid_density = 1,
grid_color = "grey50",
grid_arrowlength = 0.05,
color_by = NULL,
pt_size = 0.5,
pt_alpha = 0.6
)Arguments
- seurat_obj
Seurat object with embeddings
- zs_key
Key in misc or reductions for latent space
- vf_key
Key in misc for vector field
- embedding_key
Embedding to use (default: "umap")
- reverse
Reverse vector field direction (default: FALSE)
- n_neigh
Number of neighbors (default: 20)
- t_key
Key in metadata for pseudotime (default: NULL)
- var_transform
Variance-stabilizing transformation (default: FALSE)
- scale
Scale factor for cosine similarity (default: 10)
- self_transition
Include self-transition (default: FALSE)
- smooth
Smoothing factor for grid (default: 0.5)
- density
Display density (default: 1.0)
- grid
Show arrows on grid (default: FALSE)
- stream
Show streamplot (default: TRUE)
- stream_density
Streamline density (default: 2)
- stream_color
Streamline color (default: "black")
- stream_linewidth
Line width (default: 0.5)
- stream_arrowsize
Arrow size (default: 0.3)
- grid_density
Grid density (default: 1.0)
- grid_color
Arrow color for grid (default: "grey50")
- grid_arrowlength
Arrow length (default: 0.05)
- color_by
Variable to color points by (default: NULL)
- pt_size
Point size (default: 0.5)
- pt_alpha
Point alpha (default: 0.6)