3D-Dimensional reduction plot for cell classification visualization.

Plotting cell points on a reduced 3D space and coloring according to the groups of the cells.

Usage

CellDimPlot3D(
  srt,
  group.by,
  reduction = NULL,
  dims = c(1, 2, 3),
  axis_labs = NULL,
  palette = "Paired",
  palcolor = NULL,
  bg_color = "grey80",
  pt.size = 1.5,
  cells.highlight = NULL,
  cols.highlight = "black",
  shape.highlight = "circle-open",
  sizes.highlight = 2,
  lineages = NULL,
  lineages_palette = "Dark2",
  span = 0.75,
  width = NULL,
  height = NULL,
  save = NULL,
  force = FALSE
)

Arguments

srt: A Seurat object.
group.by: Name of one or more meta.data columns to group (color) cells by (for example, orig.ident).
reduction: Which dimensionality reduction to use. If not specified, will use the reduction returned by DefaultReduction.
dims: Dimensions to plot, must be a three-length numeric vector specifying x-, y- and z-dimensions
axis_labs: A character vector of length 3 indicating the labels for the axes.
palette: Name of a color palette name collected in SCP. Default is "Paired".
palcolor: Custom colors used to create a color palette.
bg_color: Color value for background(NA) points.
pt.size: Point size.
cells.highlight: A vector of cell names to highlight.
cols.highlight: Color used to highlight the cells.
shape.highlight: Shape of the cell to highlight. See scattergl-marker-symbol
sizes.highlight: Size of highlighted cell points.
lineages: Lineages/pseudotime to add to the plot. If specified, curves will be fitted using loess method.
lineages_palette: Color palette used for lineages.
span: A numeric value specifying the span of the loess smoother for lineages line.
width: Width in pixels, defaults to automatic sizing.
height: Height in pixels, defaults to automatic sizing.
save: The name of the file to save the plot to. Must end in ".html".
force: Whether to force drawing regardless of maximum levels in any cell group is greater than 100.

Examples

data("pancreas_sub")
pancreas_sub <- Standard_SCP(pancreas_sub)
#> [2025-09-08 16:11:26.926724] Start Standard_SCP
#> [2025-09-08 16:11:26.92698] Checking srtList... ...
#> Warning: Failed to check Seurat version compatibility: 'list' object cannot be coerced to type 'double'
#> Warning: The following arguments are not used: drop
#> Warning: The following arguments are not used: drop
#> Error in as.vector(data): no method for coercing this S4 class to a vector
CellDimPlot3D(pancreas_sub, group.by = "SubCellType", reduction = "StandardpcaUMAP3D")
#> Error in col2hex(bg_color): could not find function "col2hex"

pancreas_sub <- RunSlingshot(pancreas_sub, group.by = "SubCellType", reduction = "StandardpcaUMAP3D")
#> Warning: No shared levels found between `names(values)` of the manual scale and the data's fill values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the data's fill values.
#> Warning: Removed 8 rows containing missing values or values outside the scale range (`geom_path()`).
#> Warning: Removed 8 rows containing missing values or values outside the scale range (`geom_path()`).
#> Error in gtable_add_grob(gtable, grob, t = mean(gtable$layout[grep("panel",     gtable$layout$name), "t"]), l = dim(gtable)[2], clip = clip): `grobs` must be a single grob or a list of grobs, not a list matrix.
CellDimPlot3D(pancreas_sub, group.by = "SubCellType", reduction = "StandardpcaUMAP3D", lineages = "Lineage1")
#> Error in col2hex(bg_color): could not find function "col2hex"

3D-Dimensional reduction plot for cell classification visualization.

Usage

Arguments

See also

Examples