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Seurat (version 2.0.0)

DimPlot: Dimensional reduction plot

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

Value

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