DimPlot: Dimensional reduction plot

In nukappa/seurat_v2: Seurat : R toolkit for single cell genomics

Description

Graphs the output of a dimensional reduction technique (PCA by default). Cells are colored by their identity class.

Usage

DimPlot(object, reduction.use = "pca", dim.1 = 1, dim.2 = 2,
  cells.use = NULL, pt.size = 3, do.return = FALSE, do.bare = FALSE,
  cols.use = NULL, group.by = "ident", pt.shape = NULL,
  do.label = FALSE, label.size = 1, no.legend = FALSE)

Arguments

object	Seurat object
reduction.use	Which dimensionality reduction to use. Default is "pca", can also be "tsne", or "ica", assuming these are precomputed.
dim.1	Dimension for x-axis (default 1)
dim.2	Dimension for y-axis (default 2)
cells.use	Vector of cells to plot (default is all cells)
pt.size	Adjust point size for plotting
do.return	Return a ggplot2 object (default : FALSE)
do.bare	Do only minimal formatting (default : FALSE)
cols.use	Vector of colors, each color corresponds to an identity class. By default, ggplot assigns colors.
group.by	Group (color) cells in different ways (for example, orig.ident)
pt.shape	If NULL, all points are circles (default). You can specify any cell attribute (that can be pulled with FetchData) allowing for both different colors and different shapes on cells.
do.label	Whether to label the clusters
label.size	Sets size of labels
no.legend	Setting to TRUE will remove the legend

Value

If do.return==TRUE, returns a ggplot2 object. Otherwise, only graphical output.

nukappa/seurat_v2 documentation built on May 24, 2019, 9:57 a.m.