This function creates a velocity plot for a given Seurat object. The plot shows the velocity vectors of the cells in a specified reduction space.
Usage
VelocityPlot(
srt,
reduction,
dims = c(1, 2),
cells = NULL,
velocity = "stochastic",
plot_type = c("raw", "grid", "stream"),
group_by = NULL,
group_palette = "Paired",
group_palcolor = NULL,
n_neighbors = ceiling(ncol(srt@assays[[1]])/50),
density = 1,
smooth = 0.5,
scale = 1,
min_mass = 1,
cutoff_perc = 5,
arrow_angle = 20,
arrow_color = "black",
streamline_L = 5,
streamline_minL = 1,
streamline_res = 1,
streamline_n = 15,
streamline_width = c(0, 0.8),
streamline_alpha = 1,
streamline_color = NULL,
streamline_palette = "RdYlBu",
streamline_palcolor = NULL,
streamline_bg_color = "white",
streamline_bg_stroke = 0.5,
aspect.ratio = 1,
title = "Cell velocity",
subtitle = NULL,
xlab = NULL,
ylab = NULL,
legend.position = "right",
legend.direction = "vertical",
theme_use = "theme_scop",
theme_args = list(),
return_layer = FALSE,
seed = 11
)Arguments
- srt
A Seurat object.
- reduction
Name of the reduction in the Seurat object to use for plotting.
- dims
Indices of the dimensions to use for plotting.
- cells
Cells to include in the plot. If `NULL`, all cells will be included.
- velocity
Name of the velocity to use for plotting. Default is `"stochastic"`.
- plot_type
Type of plot to create. Can be `"raw"`, `"grid"`, or `"stream"`.
- group_by
Name of the column in the Seurat object metadata to group the cells by. Defaults is `NULL`.
- group_palette
Name of the palette to use for coloring the groups. Defaults is `"Paired"`.
- group_palcolor
Colors to use for coloring the groups. Defaults is `NULL`.
- n_neighbors
Number of neighbors to include for the density estimation. Defaults is `ceiling(ncol(srt@assays[[1]]) / 50)`.
- density
Propotion of cells to plot. Defaults is `1` (plot all cells).
- smooth
Smoothing parameter for density estimation. Defaults is `0.5`.
- scale
Scaling factor for the velocity vectors. Defaults is `1`.
- min_mass
Minimum mass value for the density-based cutoff. Defaults is `1`.
- cutoff_perc
Percentile value for the density-based cutoff. Defaults is `5`.
- arrow_angle
Angle of the arrowheads. Defaults is `20`.
- arrow_color
Color of the arrowheads. Defaults is `"black"`.
- streamline_L
Length of the streamlines. Defaults is `5`.
- streamline_minL
Minimum length of the streamlines. Defaults is `1`.
- streamline_res
Resolution of the streamlines. Defaults is `1`.
- streamline_n
Number of streamlines to plot. Defaults is `15`.
- streamline_width
Width of the streamlines. Defaults is `c(0, 0.8)`.
- streamline_alpha
Alpha transparency of the streamlines. Defaults is `1`.
- streamline_color
Color of the streamlines. Defaults is `NULL`.
- streamline_palette
Name of the palette to use for coloring the streamlines. Defaults is `"RdYlBu"`.
- streamline_palcolor
Colors to use for coloring the streamlines. Defaults is `NULL`.
- streamline_bg_color
Background color of the streamlines. Defaults is `"white"`.
- streamline_bg_stroke
Stroke width of the streamlines background. Defaults is `0.5`.
- aspect.ratio
Aspect ratio of the plot. Defaults is `1`.
- title
Title of the plot. Defaults is `"Cell velocity"`.
- subtitle
Subtitle of the plot. Defaults is `NULL`.
- xlab
x-axis label. Defaults is `NULL`.
- ylab
y-axis label. Defaults is `NULL`.
- legend.position
Position of the legend. Defaults is `"right"`.
- legend.direction
Direction of the legend. Defaults is `"vertical"`.
- theme_use
Name of the theme to use for plotting. Defaults is `"theme_scop"`.
- theme_args
List of theme arguments for customization. Defaults is `list()`.
- return_layer
Whether to return the plot layers as a list. Defaults is `FALSE`.
- seed
Random seed for reproducibility. Defaults is `11`.
Examples
if (FALSE) { # \dontrun{
data(pancreas_sub)
pancreas_sub <- standard_scop(pancreas_sub)
pancreas_sub <- RunSCVELO(
pancreas_sub,
group_by = "SubCellType",
linear_reduction = "pca",
nonlinear_reduction = "umap",
return_seurat = TRUE
)
VelocityPlot(
pancreas_sub,
reduction = "UMAP"
)
VelocityPlot(
pancreas_sub,
reduction = "UMAP",
group_by = "SubCellType"
)
VelocityPlot(
pancreas_sub,
reduction = "UMAP",
plot_type = "grid"
)
VelocityPlot(
pancreas_sub,
reduction = "UMAP",
plot_type = "stream"
)
VelocityPlot(
pancreas_sub,
reduction = "UMAP",
plot_type = "stream",
streamline_color = "black"
)
VelocityPlot(
pancreas_sub,
reduction = "UMAP",
plot_type = "stream",
streamline_color = "black",
arrow_color = "red"
)
} # }