Visualize 'features' on a dimensional reduction plot

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,
  dims = c(1, 2),
  cells = NULL,
  cols = if (blend) {
     c("lightgrey", "#ff0000", "#00ff00")
 } else {
    
    c("lightgrey", "blue")
 },
  pt.size = NULL,
  alpha = 1,
  stroke.size = NULL,
  order = FALSE,
  min.cutoff = NA,
  max.cutoff = NA,
  reduction = NULL,
  split.by = NULL,
  keep.scale = "feature",
  shape.by = NULL,
  slot = "data",
  assay = NULL,
  blend = FALSE,
  blend.threshold = 0.5,
  label = FALSE,
  label.size = 4,
  label.color = "black",
  repel = FALSE,
  ncol = NULL,
  coord.fixed = FALSE,
  by.col = TRUE,
  sort.cell = deprecated(),
  interactive = FALSE,
  combine = TRUE,
  raster = NULL,
  raster.dpi = c(512, 512)
)

Arguments

object

Seurat object

features

Vector of features to plot. Features can come from:

An Assay feature (e.g. a gene name - "MS4A1")
A column name from meta.data (e.g. mitochondrial percentage - "percent.mito")
A column name from a DimReduc object corresponding to the cell embedding values (e.g. the PC 1 scores - "PC_1")

dims

Dimensions to plot, must be a two-length numeric vector specifying x- and y-dimensions

cells

Vector of cells to plot (default is all cells)

cols

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. When blend is TRUE, takes anywhere from 1-3 colors:

1 color:: Treated as color for double-negatives, will use default colors 2 and 3 for per-feature expression
2 colors:: Treated as colors for per-feature expression, will use default color 1 for double-negatives
3+ colors:: First color used for double-negatives, colors 2 and 3 used for per-feature expression, all others ignored

pt.size

Adjust point size for plotting

alpha

Alpha value for plotting (default is 1)

stroke.size

Adjust stroke (outline) size of points

order

Boolean determining whether to plot cells in order of expression. Can be useful if cells expressing given feature are getting buried.

min.cutoff, max.cutoff

Vector of minimum and maximum cutoff values for each feature, may specify quantile in the form of 'q##' where '##' is the quantile (eg, 'q1', 'q10')

reduction

Which dimensionality reduction to use. If not specified, first searches for umap, then tsne, then pca

split.by

A factor in object metadata to split the plot by, pass 'ident' to split by cell identity

keep.scale

How to handle the color scale across multiple plots. Options are:

“feature” (default; by row/feature scaling): The plots for each individual feature are scaled to the maximum expression of the feature across the conditions provided to split.by
“all” (universal scaling): The plots for all features and conditions are scaled to the maximum expression value for the feature with the highest overall expression
NULL (no scaling): Each individual plot is scaled to the maximum expression value of the feature in the condition provided to split.by. Be aware setting NULL will result in color scales that are not comparable between plots

shape.by

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. Only applicable if raster = FALSE.

slot

Which slot to pull expression data from?

assay

Primary assay to pull feature data from

blend

Scale and blend expression values to visualize coexpression of two features

blend.threshold

The color cutoff from weak signal to strong signal; ranges from 0 to 1.

label

Whether to label the clusters

label.size

Sets size of labels

label.color

Sets the color of the label text

repel

Repel labels

ncol

Number of columns to combine multiple feature plots to, ignored if split.by is not NULL

coord.fixed

Plot cartesian coordinates with fixed aspect ratio

by.col

If splitting by a factor, plot the splits per column with the features as rows; ignored if blend = TRUE

sort.cell

Redundant with order. This argument is being deprecated. Please use order instead.

interactive

Launch an interactive FeaturePlot

combine

Combine plots into a single patchworked ggplot object. If FALSE, return a list of ggplot objects

raster

Convert points to raster format, default is NULL which automatically rasterizes if plotting more than 100,000 cells

raster.dpi

Pixel resolution for rasterized plots, passed to geom_scattermore(). Default is c(512, 512).

Value

A patchworked ggplot object if combine = TRUE; otherwise, a list of ggplot objects

Note

For the old do.hover and do.identify functionality, please see HoverLocator and CellSelector, respectively.

Examples

data("pbmc_small")
FeaturePlot(object = pbmc_small, features = 'PC_1')