FeaturePlot: Visualize 'features' on a dimensional reduction plot

In mayer-lab/SeuratForMayer2018: Seurat : R Toolkit for Single Cell Genomics

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

FeaturePlot(object, features.plot, min.cutoff = NA, max.cutoff = NA,
  dim.1 = 1, dim.2 = 2, cells.use = NULL, pt.size = 1,
  cols.use = c("yellow", "red"), pch.use = 16, overlay = FALSE,
  do.hover = FALSE, data.hover = "ident", do.identify = FALSE,
  reduction.use = "tsne", use.imputed = FALSE, nCol = NULL,
  no.axes = FALSE, no.legend = TRUE, dark.theme = FALSE,
  do.return = FALSE)

Arguments

object	Seurat object
features.plot	Vector of features to plot
min.cutoff	Vector of minimum cutoff values for each feature, may specify quantile in the form of 'q##' where '##' is the quantile (eg, 1, 10)
max.cutoff	Vector of maximum cutoff values for each feature, may specify quantile in the form of 'q##' where '##' is the quantile (eg, 1, 10)
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	The two colors to form the gradient over. Provide as string vector with the first color corresponding to low values, the second to high. Also accepts a Brewer color scale or vector of colors. Note: this will bin the data into number of colors provided.
pch.use	Pch for plotting
overlay	Plot two features overlayed one on top of the other
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 identity. Pass 'NULL' to remove extra data.
do.identify	Opens a locator session to identify clusters of cells
reduction.use	Which dimensionality reduction to use. Default is "tsne", can also be "pca", or "ica", assuming these are precomputed.
use.imputed	Use imputed values for gene expression (default is FALSE)
nCol	Number of columns to use when plotting multiple features.
no.axes	Remove axis labels
no.legend	Remove legend from the graph. Default is TRUE.
dark.theme	Plot in a dark theme
do.return	return the ggplot2 object

Value

No return value, only a graphical output

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