R/visualization.R, R/convenience.RSpatialPlot.RdSpatialPlot 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 )
| 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 |
| 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 |
| do.identify, do.hover | DEPRECATED in favor of |
| identify.ident | DEPRECATED |
| information | An optional dataframe or matrix of extra information to be displayed on hover |
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
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") }