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Pseudotime Projection Plot

Source: R/PseudotimeProjectionPlot.R
PseudotimeProjectionPlot.Rd

Creates a projection plot similar to VelocityPlot, but uses pseudotime data instead of RNA velocity analysis results.

Usage

PseudotimeProjectionPlot(
  srt,
  reduction,
  time_key,
  dims = c(1, 2),
  cells = NULL,
  method = c("knn", "gradient"),
  k = 30,
  graph_name = NULL,
  plot_type = c("raw", "grid", "stream"),
  group.by = NULL,
  group_palette = "Chinese",
  group_palcolor = NULL,
  n_neighbors = ceiling(ncol(srt@assays[[1]])/50),
  density = 2,
  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 = "Pseudotime projection",
  subtitle = NULL,
  xlab = NULL,
  ylab = NULL,
  legend.position = "right",
  legend.direction = "vertical",
  theme_use = "theme_scop",
  theme_args = list(),
  return_layer = FALSE,
  palette = NULL,
  palcolor = NULL,
  show_cells = TRUE,
  pt.size = 2,
  pt.alpha = 0.3,
  label = NULL,
  label.size = 4,
  label.fg = "black",
  label.bg = "white",
  label.bg.r = 0.1,
  seed = 11,
  verbose = TRUE
)

Arguments

srt

A Seurat object.

reduction

Reduction to plot. NULL uses DefaultReduction.

time_key

Name of the column in the Seurat object metadata containing pseudotime values.

dims

Length-2 vector of dimensions to plot.

cells

Cell names to include.

method

Method to compute velocity vectors from pseudotime. Can be "gradient" or "knn".

k

Number of nearest neighbors to use when method = "knn".

graph_name

Name of the KNN graph in the Seurat object to use. If NULL, a new graph will be computed. Default is NULL.

plot_type

Type of plot to create. Can be "raw", "grid", or "stream".

group.by

Metadata column(s) used to color cells.

group_palette

Name of the palette to use for coloring the groups. Defaults is "Chinese".

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

Scale for the streamline grid (number of points per axis is ceiling(50 * density)). Default is 2 (CellRank/scvelo-style).

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, streamline_minL, streamline_res, streamline_n, streamline_width, streamline_alpha, streamline_color, streamline_palette, streamline_palcolor, streamline_bg_color, streamline_bg_stroke

Streamline appearance for velocity plots.

aspect.ratio

Panel aspect ratio.

title

The text for the title. Defaults is "Pseudotime projection".

subtitle

Plot subtitle.

xlab

Label for the x axis.

ylab

Label for the y axis.

legend.position

Legend position passed to theme().

legend.direction

Legend direction passed to theme().

theme_use, theme_args

Theme name or function, plus extra theme arguments.

return_layer

Whether to return the plot layers as a list. Defaults is FALSE.

palette

Deprecated alias of group_palette.

palcolor

Deprecated alias of group_palcolor.

show_cells

Whether to show cell points on the plot. Defaults is TRUE.

pt.size

Size of cell points. Defaults is 2 (CellRank-style overlapping patches).

pt.alpha

The transparency of the data points. Default is 0.3 (CellRank/scvelo-style).

label

Whether to label the cell groups. Defaults is TRUE when group.by is specified.

label.size

Group labels. label_insitu = FALSE uses numbers instead of group names.

label.fg

Foreground color of labels. Defaults is "black".

label.bg

Background color of labels. Defaults is "white".

label.bg.r

Group labels. label_insitu = FALSE uses numbers instead of group names.

seed

Random seed.

verbose

Whether to print messages.

See also

VelocityPlot, CellDimPlot

Examples

data(pancreas_sub)
pancreas_sub <- RunStandardWorkflow(pancreas_sub)
#> ℹ [2026-08-30 04:46:25] Start standard processing workflow...
#> ℹ [2026-08-30 04:46:25] Checking a list of <Seurat>...
#> ! [2026-08-30 04:46:25] Data 1/1 of the `srt_list` is "unknown"
#> Warning: Data 1/1 of the `srt_list` is "unknown"
#> ℹ [2026-08-30 04:46:25] Perform `NormalizeData()` with `normalization.method = 'LogNormalize'` on 1/1 of `srt_list`...
#> ℹ [2026-08-30 04:46:25] Perform `FindVariableFeatures()` on 1/1 of `srt_list`...
#> ℹ [2026-08-30 04:46:25] Use the separate HVF from `srt_list`
#> ℹ [2026-08-30 04:46:25] Number of available HVF: 2000
#> ℹ [2026-08-30 04:46:25] Finished check
#> ℹ [2026-08-30 04:46:25] Perform `ScaleData()`
#> ℹ [2026-08-30 04:46:25] Perform pca linear dimension reduction
#> ℹ [2026-08-30 04:46:26] Use stored estimated dimensions 1:23 for Standardpca
#> ℹ [2026-08-30 04:46:26] Perform `Seurat::FindClusters()` with `cluster_algorithm = 'louvain'` and `cluster_resolution = 0.6`
#> ℹ [2026-08-30 04:46:26] Reorder clusters...
#> ℹ [2026-08-30 04:46:26] Skip `log1p()` because `layer = data` is not "counts"
#> ℹ [2026-08-30 04:46:26] Perform umap nonlinear dimension reduction
#> ✔ [2026-08-30 04:46:34] Standard processing workflow completed
pancreas_sub <- RunSlingshot(
  pancreas_sub,
  reduction = "UMAP",
  group.by = "SubCellType"
)
#> Warning: Removed 7 rows containing missing values or values outside the scale range
#> (`geom_path()`).
#> Warning: Removed 7 rows containing missing values or values outside the scale range
#> (`geom_path()`).


PseudotimeProjectionPlot(
  pancreas_sub,
  reduction = "UMAP",
  group.by = "SubCellType",
  time_key = "Lineage1",
  method = "gradient",
  plot_type = "raw"
)
#> ! [2026-08-30 04:46:35] Removed 328 cells with NA pseudotime values
#> Warning: Removed 328 cells with NA pseudotime values


PseudotimeProjectionPlot(
  pancreas_sub,
  reduction = "UMAP",
  time_key = "Lineage1",
  group.by = "SubCellType",
  plot_type = "stream",
  show_cells = TRUE,
  label = TRUE
)
#> ! [2026-08-30 04:46:35] Removed 328 cells with NA pseudotime values
#> Warning: Removed 328 cells with NA pseudotime values
#> ℹ [2026-08-30 04:46:35] Computing KNN graph from embedding...


PseudotimeProjectionPlot(
  pancreas_sub,
  reduction = "UMAP",
  time_key = "Lineage2",
  plot_type = "grid"
)
#> ! [2026-08-30 04:46:37] Removed 244 cells with NA pseudotime values
#> Warning: Removed 244 cells with NA pseudotime values
#> ℹ [2026-08-30 04:46:37] Computing KNN graph from embedding...


PseudotimeProjectionPlot(
  pancreas_sub,
  reduction = "UMAP",
  time_key = "Lineage1",
  method = "gradient",
  plot_type = "raw"
)
#> ! [2026-08-30 04:46:39] Removed 328 cells with NA pseudotime values
#> Warning: Removed 328 cells with NA pseudotime values