Spatial neighborhood plot — SpatialNeighborhoodPlot • scop

Visualize results produced by RunSpatialNeighborhood() using scop spatial, statistical, and network plotting conventions.

Usage

SpatialNeighborhoodPlot(
  srt,
  method = NULL,
  plot_type = c("heatmap", "network", "stat", "spatial"),
  comparison = NULL,
  condition = NULL,
  value = c("estimate", "fraction", "count"),
  FDR_threshold = 0.05,
  top_n = 30,
  layout = c("fr", "nicely", "kk", "circle", "mds"),
  edge_size = c(0.4, 2),
  cols.enriched = "#d7301f",
  cols.depleted = "#2b8cbe",
  cols.ns = "grey75",
  pair = NULL,
  image = NULL,
  overlay_image = TRUE,
  coord.cols = c("col", "row"),
  split.by = NULL,
  palette = "RdBu",
  palcolor = NULL,
  legend.position = "right",
  legend.direction = "vertical",
  legend.title = NULL,
  theme_use = "theme_scop",
  theme_args = list(),
  combine = TRUE,
  nrow = NULL,
  ncol = NULL,
  byrow = TRUE,
  seed = 11,
  verbose = TRUE,
  ...
)

Arguments

srt: A Seurat object.
method: Stored neighborhood method to plot. If NULL, the active method is used.
plot_type: Plot type. One of "heatmap", "network", "stat", or "spatial".
comparison, condition: Optional filters for stored result tables.
value: Column used as the plotted effect value.
FDR_threshold: FDR cutoff used to mark significant pairs.
top_n: Number of pairs to show for network and statistic plots.
layout: Network layout.
edge_size: Network edge size range.
cols.enriched, cols.depleted, cols.ns: Colors for direction categories.
pair: Pair to visualize for plot_type = "spatial", either "from|to" or a length-2 character vector.
image: Name of the Seurat spatial image. If NULL, the first image is used when present.
overlay_image: Whether to draw the spatial image beneath spots.
coord.cols: Metadata coordinate columns used when no Seurat image coordinates are available.
split.by: Optional metadata column identifying conditions for differential neighborhood statistics.
palette: Color palette name. Available palettes can be found in thisplot::show_palettes. Default is "Chinese".
palcolor: Custom colors used to create a color palette. Default is NULL.
legend.position: The position of legends, one of "none", "left", "right", "bottom", "top". Default is "right".
legend.direction: The direction of the legend in the plot. Can be one of "vertical" or "horizontal".
legend.title: Title for the legend. Default is NULL, which uses the group name.
theme_use: Theme used. Can be a character string or a theme function. Default is "theme_scop".
theme_args: Other arguments passed to the theme_use. Default is list().
combine: Combine plots into a single patchwork object. If FALSE, return a list of ggplot objects.
nrow: Number of rows in the combined plot. Default is NULL, which means determined automatically based on the number of plots.
ncol: Number of columns in the combined plot. Default is NULL, which means determined automatically based on the number of plots.
byrow: Whether to arrange the plots by row in the combined plot. Default is TRUE.
seed: Random seed used by layouts and jittered plot layers.
verbose: Whether to print the message. Default is TRUE.
...: Additional arguments passed to the selected backend.

Value

A ggplot, patchwork, or list of ggplot objects.

Examples

data(visium_human_pancreas_sub)
spatial <- visium_human_pancreas_sub
spatial <- RunSpatialNeighborhood(
  spatial,
  group.by = "coda_label",
  coord.cols = c("x", "y"),
  k = 4,
  verbose = FALSE
)

SpatialNeighborhoodPlot(spatial, plot_type = "heatmap")

SpatialNeighborhoodPlot(spatial, plot_type = "network", top_n = 12)
#> Error in calcCurveGrob(x, x$debug): end points must not be identical
SpatialNeighborhoodPlot(spatial, plot_type = "stat", top_n = 12)

SpatialNeighborhoodPlot(
  spatial,
  plot_type = "spatial",
  overlay_image = FALSE,
  coord.cols = c("x", "y")
)