Colors single cells on a dimensional reduction plot according to a 'feature' (i.e. gene expression, PC scores, number of genes detected, etc.)
FeaturePlot( object, features, dims = c(1, 2), cells = NULL, cols = if (blend) { c("lightgrey", "#ff0000", "#00ff00") } else { c("lightgrey", "blue") }, pt.size = NULL, order = FALSE, min.cutoff = NA, max.cutoff = NA, reduction = NULL, split.by = NULL, keep.scale = "feature", shape.by = NULL, slot = "data", blend = FALSE, blend.threshold = 0.5, label = FALSE, label.size = 4, repel = FALSE, ncol = NULL, coord.fixed = FALSE, by.col = TRUE, sort.cell = NULL, interactive = FALSE, combine = TRUE, raster = NULL )
object | Seurat object |
---|---|
features | Vector of features to plot. Features can come from:
|
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
|
pt.size | Adjust point size for plotting |
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 feature plot by, pass 'ident' to split by cell identity'; similar to the old |
keep.scale | How to handle the color scale across multiple plots. Options are:
|
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 |
slot | Which slot to pull expression 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 |
repel | Repel labels |
ncol | Number of columns to combine multiple feature plots to, ignored if |
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 |
sort.cell | Redundant with |
interactive | Launch an interactive |
combine | Combine plots into a single |
raster | Convert points to raster format, default is |
A patchworked
ggplot object if combine = TRUE
; otherwise, a list of ggplot objects
For the old do.hover
and do.identify
functionality, please see HoverLocator
and CellSelector
, respectively.