Plot spatial graphs — plotColGraph • Voyager

A ggplot version of spdep::plot.nb, reducing boilerplate for SFE objects.

Usage

plotColGraph(
  sfe,
  colGraphName = 1L,
  colGeometryName = 1L,
  sample_id = "all",
  weights = FALSE,
  segment_size = 0.5,
  geometry_size = 0.5,
  ncol = NULL,
  bbox = NULL
)

plotAnnotGraph(
  sfe,
  annotGraphName = 1L,
  annotGeometryName = 1L,
  sample_id = "all",
  weights = FALSE,
  segment_size = 0.5,
  geometry_size = 0.5,
  ncol = NULL,
  bbox = NULL
)

Arguments

sfe: A SpatialFeatureExperiment object.
colGraphName: Name of graph associated with columns of the gene count matrix to be plotted.
colGeometryName: Name of a colGeometry sf data frame whose numeric columns of interest are to be used to compute the metric. Use colGeometryNames to look up names of the sf data frames associated with cells/spots.
sample_id: Sample(s) in the SFE object whose cells/spots to use. Can be "all" to compute metric for all samples; the metric is computed separately for each sample.
weights: Whether to plot weights. If TRUE, then transparency (alpha) of the segments will represent edge weights.
segment_size: Thickness of the segments that represent graph edges.
geometry_size: Point size (for POINT geometries) or line thickness (for LINESTRING and POLYGON) to plot the geometry in the background.
ncol: Number of columns if plotting multiple features. Defaults to NULL, which means using the same logic as facet_wrap, which is used by patchwork's wrap_plots by default.
bbox: A bounding box to specify a smaller region to plot, useful when the dataset is large. Can be a named numeric vector with names "xmin", "xmax", "ymin", and "ymax", in any order. If plotting multiple samples, it should be a matrix with sample IDs as column names and "xmin", "ymin", "xmax", and "ymax" as row names. If multiple samples are plotted but bbox is a vector rather than a matrix, then the same bounding box will be used for all samples. You may see points at the edge of the geometries if the intersection between the bounding box and a geometry happens to be a point there. If NULL, then the entire tissue is plotted.
annotGraphName: Name of the annotation graph to plot.
annotGeometryName: Name of the annotGeometry, which is associated with the graph specified with annotGraphName, for spatial coordinates of the graph nodes and for context.

Value

A ggplot2 object.

Examples

library(SpatialFeatureExperiment)
library(SFEData)
library(sf)
#> Linking to GEOS 3.11.0, GDAL 3.5.3, PROJ 9.1.0; sf_use_s2() is TRUE
sfe <- McKellarMuscleData("small")
#> see ?SFEData and browseVignettes('SFEData') for documentation
#> loading from cache
colGraph(sfe, "visium") <- findVisiumGraph(sfe)
plotColGraph(sfe, colGraphName = "visium", colGeometryName = "spotPoly")

# Make the myofiber segmentations a valid POLYGON geometry
ag <- annotGeometry(sfe, "myofiber_simplified")
ag <- st_buffer(ag, 0)
ag <- ag[!st_is_empty(ag), ]
annotGeometry(sfe, "myofiber_simplified") <- ag
annotGraph(sfe, "myofibers") <-
    findSpatialNeighbors(sfe,
        type = "myofiber_simplified", MARGIN = 3,
        method = "tri2nb", dist_type = "idw"
    )
#> Warning: style is M (missing); style should be set to a valid value
plotAnnotGraph(sfe,
    annotGraphName = "myofibers",
    annotGeometryName = "myofiber_simplified",
    weights = TRUE
)