Seurat: SpatialPlot – R documentation

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SpatialPlot

Visualize spatial clustering and expression data.

Description

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.

Usage

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),
  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),
  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
`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

## Not run: 
# 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")

## End(Not run)

Seurat

Tools for Single Cell Genomics

v4.0.1

GPL-3 | file LICENSE

Authors

Andrew Butler [ctb] (<https://orcid.org/0000-0003-3608-0463>), Saket Choudhary [ctb] (<https://orcid.org/0000-0001-5202-7633>), Charlotte Darby [ctb] (<https://orcid.org/0000-0003-2195-5300>), Jeff Farrell [ctb], Christoph Hafemeister [ctb] (<https://orcid.org/0000-0001-6365-8254>), Yuhan Hao [ctb] (<https://orcid.org/0000-0002-1810-0822>), Paul Hoffman [aut, cre] (<https://orcid.org/0000-0002-7693-8957>), Jaison Jain [ctb] (<https://orcid.org/0000-0002-9478-5018>), Efthymia Papalexi [ctb] (<https://orcid.org/0000-0001-5898-694X>), Patrick Roelli [ctb], Rahul Satija [ctb] (<https://orcid.org/0000-0001-9448-8833>), Karthik Shekhar [ctb], Avi Srivastava [ctb] (<https://orcid.org/0000-0001-9798-2079>), Tim Stuart [ctb] (<https://orcid.org/0000-0002-3044-0897>), Kristof Torkenczy [ctb] (<https://orcid.org/0000-0002-4869-7957>), Shiwei Zheng [ctb] (<https://orcid.org/0000-0001-6682-6743>), Satija Lab and Collaborators [fnd]

Initial release

2021-03-17