FeatureDimPlot3D: 3D-Dimensional reduction plot for gene expression...
In zh542370159/SCP: Single Cell Pipeline

FeatureDimPlot3D

R Documentation

3D-Dimensional reduction plot for gene expression visualization.

Description

Plotting cell points on a reduced 3D space and coloring according to the gene expression in the cells.

Usage

FeatureDimPlot3D(
  srt,
  features,
  reduction = NULL,
  dims = c(1, 2, 3),
  axis_labs = NULL,
  split.by = NULL,
  slot = "data",
  assay = NULL,
  calculate_coexp = FALSE,
  pt.size = 1.5,
  cells.highlight = NULL,
  cols.highlight = "black",
  shape.highlight = "circle-open",
  sizes.highlight = 2,
  width = NULL,
  height = NULL,
  save = NULL,
  force = FALSE
)

Arguments

`srt`	A Seurat object.
`features`	A character vector or a named list of features to plot. Features can be gene names in Assay or names of numeric columns in meta.data.
`reduction`	Which dimensionality reduction to use. If not specified, will use the reduction returned by `DefaultReduction`.
`dims`	Dimensions to plot, must be a two-length numeric vector specifying x- and y-dimensions.
`axis_labs`	A character vector of length 3 indicating the labels for the axes.
`split.by`	Name of a column in meta.data to split plot by.
`slot`	Which slot to pull expression data from? Default is `data`.
`assay`	Which assay to pull expression data from. If `NULL`, will use the assay returned by `DefaultAssay`.
`calculate_coexp`	Whether to calculate the co-expression value (geometric mean) of the features.
`pt.size`	Point size for plotting.
`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 cells.
`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 the number of features greater than 100.

Examples

data("pancreas_sub")
pancreas_sub <- Standard_SCP(pancreas_sub)
FeatureDimPlot3D(pancreas_sub, features = c("Ghrl", "Ins1", "Gcg", "Ins2"), reduction = "StandardpcaUMAP3D")
FeatureDimPlot3D(pancreas_sub, features = c("StandardPC_1", "StandardPC_2"), reduction = "StandardpcaUMAP3D")

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