CellDimPlot3D: 3D-Dimensional reduction plot for cell classification...
In zh542370159/SCP: Single Cell Pipeline

CellDimPlot3D

R Documentation

3D-Dimensional reduction plot for cell classification visualization.

Description

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)
CellDimPlot3D(pancreas_sub, group.by = "SubCellType", reduction = "StandardpcaUMAP3D")

pancreas_sub <- RunSlingshot(pancreas_sub, group.by = "SubCellType", reduction = "StandardpcaUMAP3D")
CellDimPlot3D(pancreas_sub, group.by = "SubCellType", reduction = "StandardpcaUMAP3D", lineages = "Lineage1")

zh542370159/SCP documentation built on Nov. 22, 2023, 2:34 a.m.