DimPlot: Dimensional reduction plot

In mayer-lab/SeuratForMayer2018: 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.hover = FALSE, data.hover = "ident", do.identify = FALSE,
  do.label = FALSE, label.size = 1, no.legend = FALSE, no.axes = FALSE,
  dark.theme = 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.hover	Enable hovering over points to view information
data.hover	Data to add to the hover, pass a character vector of features to add. Defaults to cell name and ident. Pass 'NULL' to clear extra information.
do.identify	Opens a locator session to identify clusters of cells.
do.label	Whether to label the clusters
label.size	Sets size of labels
no.legend	Setting to TRUE will remove the legend
no.axes	Setting to TRUE will remove the axes
dark.theme	Use a dark theme for the plot
...	Extra parameters to FeatureLocator for do.identify = TRUE

Value

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

See Also

FeatureLocator

mayer-lab/SeuratForMayer2018 documentation built on May 25, 2019, 9:34 p.m.