Seurat (version 1.2.1)

feature.plot: Visualize 'features' on a dimensional reduction plot

Description

Colors single cells on a dimensional reduction plot according to a 'feature' (i.e. gene expression, PC scores, number of genes detected, etc.)

Usage

feature.plot(object, features.plot, dim.1 = 1, dim.2 = 2, cells.use = NULL, pt.size = 1, cols.use = heat.colors(10), pch.use = 16, reduction.use = "tsne", nCol = NULL)

Arguments

object

Seurat object

features.plot

Vector of features to plot

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

cols.use

Ordered vector of colors to use for plotting. Default is heat.colors(10).

pch.use

Pch for plotting

reduction.use

Which dimensionality reduction to use. Default is "tsne", can also be "pca", or "ica", assuming these are precomputed.

nCol

Number of columns to use when plotting multiple features.

Value

No return value, only a graphical output

Details

To determine the color, the feature values across all cells are placed into discrete bins, and then assigned a color based on cols.use. The number of bins is determined by the number of colors in cols.use