dim.plot: Dimensional reduction plot

Description Usage Arguments Value

Description

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

Usage

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dim.plot(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)

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 fetch.data) allowing for both different colors and different shapes on cells.

Value

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


paodan/studySeu documentation built on May 23, 2019, 3:06 p.m.