Visualize spatial clustering and expression data.

SpatialPlot plots a feature or discrete grouping (e.g. cluster assignments) as spots over the image that was collected. We also provide SpatialFeaturePlot and SpatialDimPlot as wrapper functions around SpatialPlot for a consistent naming framework.

SpatialPlot(
  object,
  group.by = NULL,
  features = NULL,
  images = NULL,
  cols = NULL,
  image.alpha = 1,
  crop = TRUE,
  slot = "data",
  min.cutoff = NA,
  max.cutoff = NA,
  cells.highlight = NULL,
  cols.highlight = c("#DE2D26", "grey50"),
  facet.highlight = FALSE,
  label = FALSE,
  label.size = 5,
  label.color = "white",
  label.box = TRUE,
  repel = FALSE,
  ncol = NULL,
  combine = TRUE,
  pt.size.factor = 1.6,
  alpha = c(1, 1),
  stroke = 0.25,
  interactive = FALSE,
  do.identify = FALSE,
  identify.ident = NULL,
  do.hover = FALSE,
  information = NULL
)

SpatialDimPlot(
  object,
  group.by = NULL,
  images = NULL,
  cols = NULL,
  crop = TRUE,
  cells.highlight = NULL,
  cols.highlight = c("#DE2D26", "grey50"),
  facet.highlight = FALSE,
  label = FALSE,
  label.size = 7,
  label.color = "white",
  repel = FALSE,
  ncol = NULL,
  combine = TRUE,
  pt.size.factor = 1.6,
  alpha = c(1, 1),
  image.alpha = 1,
  stroke = 0.25,
  label.box = TRUE,
  interactive = FALSE,
  information = NULL
)

SpatialFeaturePlot(
  object,
  features,
  images = NULL,
  crop = TRUE,
  slot = "data",
  min.cutoff = NA,
  max.cutoff = NA,
  ncol = NULL,
  combine = TRUE,
  pt.size.factor = 1.6,
  alpha = c(1, 1),
  image.alpha = 1,
  stroke = 0.25,
  interactive = FALSE,
  information = NULL
)

Arguments

object: A Seurat object
group.by: Name of meta.data column to group the data by
features: Name of the feature to visualize. Provide either group.by OR features, not both.
images: Name of the images to use in the plot(s)
cols: Vector of colors, each color corresponds to an identity class. This may also be a single character or numeric value corresponding to a palette as specified by brewer.pal.info. By default, ggplot2 assigns colors
image.alpha: Adjust the opacity of the background images. Set to 0 to remove.
crop: Crop the plot in to focus on points plotted. Set to FALSE to show entire background image.
slot: If plotting a feature, which data slot to pull from (counts, data, or scale.data)
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')
cells.highlight: A list of character or numeric vectors of cells to highlight. If only one group of cells desired, can simply pass a vector instead of a list. If set, colors selected cells to the color(s) in cols.highlight
cols.highlight: A vector of colors to highlight the cells as; ordered the same as the groups in cells.highlight; last color corresponds to unselected cells.
facet.highlight: When highlighting certain groups of cells, split each group into its own plot
label: Whether to label the clusters
label.size: Sets the size of the labels
label.color: Sets the color of the label text
label.box: Whether to put a box around the label text (geom_text vs geom_label)
repel: Repels the labels to prevent overlap
ncol: Number of columns if plotting multiple plots
combine: Combine plots into a single gg object; note that if TRUE; themeing will not work when plotting multiple features/groupings
pt.size.factor: Scale the size of the spots.
alpha: Controls opacity of spots. Provide as a vector specifying the min and max for SpatialFeaturePlot. For SpatialDimPlot, provide a single alpha value for each plot.
stroke: Control the width of the border around the spots
interactive: Launch an interactive SpatialDimPlot or SpatialFeaturePlot session, see ISpatialDimPlot or ISpatialFeaturePlot for more details
do.identify, do.hover: DEPRECATED in favor of interactive
identify.ident: DEPRECATED
information: An optional dataframe or matrix of extra information to be displayed on hover

Value

If do.identify, either a vector of cells selected or the object with selected cells set to the value of identify.ident (if set). Else, if do.hover, a plotly object with interactive graphics. Else, a ggplot object

Examples

if (FALSE) {
# For functionality analagous to FeaturePlot
SpatialPlot(seurat.object, features = "MS4A1")
SpatialFeaturePlot(seurat.object, features = "MS4A1")

# For functionality analagous to DimPlot
SpatialPlot(seurat.object, group.by = "clusters")
SpatialDimPlot(seurat.object, group.by = "clusters")
}