plotSpatialContext: Plot spatial context graph

In BodenmillerGroup/imcRtools: Methods for imaging mass cytometry data analysis

Plot spatial context graph

Description

Function to plot directed spatial context graphs based on symbolic edge-lists and vertex metadata, which operates on the cohort-level. The user can specify node, node_label and edge aesthetics.

Usage

plotSpatialContext(
  object,
  entry = "spatial_context",
  group_by = "sample_id",
  node_color_by = NULL,
  node_size_by = NULL,
  node_color_fix = NULL,
  node_size_fix = NULL,
  node_label_repel = TRUE,
  node_label_color_by = NULL,
  node_label_color_fix = NULL,
  draw_edges = TRUE,
  edge_color_fix = NULL,
  return_data = FALSE
)

Arguments

object	a SingleCellExperiment or SpatialExperiment object.
entry	single character specifying the colData(object) entry containing the detectSpatialContext output. Defaults to "spatial_context".
group_by	a single character indicating the colData(object) entry by which SCs are grouped. This is usually the image or patient ID. Defaults to "sample_id".
node_color_by	single character either NULL, "name","n_cells", "n_group" by which the nodes should be colored.
node_size_by	single character either NULL, "n_cells","n_group" by which the size of the nodes are defined.
node_color_fix	single character specifying the color of all nodes.
node_size_fix	single numeric specifying the size of all nodes.
node_label_repel	should nodes be labelled? Defaults to TRUE.
node_label_color_by	single character either NULL, "name","n_cells","n_group" by which the node labels should be colored.
node_label_color_fix	single character specifying the color of all node labels.
draw_edges	should edges be drawn between nodes? Defaults to TRUE.
edge_color_fix	single character specifying the color of all edges.
return_data	should the edge list and vertex metadata for graph construction be returned as a list of two data.frames?

Value

returns a ggplot object or a list of two data.frames.

Author(s)

Lasse Meyer ([e-mail])

References

Bhate S. et al., Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors, Cell Systems, 2022

See Also

detectSpatialContext for the function to detect spatial contexts

filterSpatialContext for the function to filter spatial contexts

Examples

set.seed(22)
library(cytomapper)
data(pancreasSCE)

## 1. Cellular neighborhood (CN)
sce <- buildSpatialGraph(pancreasSCE, img_id = "ImageNb",
                        type = "knn",
                        name = "knn_cn_graph",
                        k = 5)

sce <- aggregateNeighbors(sce, colPairName = "knn_cn_graph",
                         aggregate_by = "metadata",
                         count_by = "CellType",
                         name = "aggregatedCellTypes")

cur_cluster <- kmeans(sce$aggregatedCellTypes, centers = 3)
sce$cellular_neighborhood <- factor(cur_cluster$cluster)

plotSpatial(sce, img_id = "ImageNb",
           colPairName = "knn_cn_graph",
           node_color_by = "cellular_neighborhood",
           scales = "free")

## 2. Spatial context (SC)
sce <- buildSpatialGraph(sce, img_id = "ImageNb",
                        type = "knn",
                        name = "knn_sc_graph",
                        k = 15)

sce <- aggregateNeighbors(sce, colPairName = "knn_sc_graph",
                         aggregate_by = "metadata",
                         count_by = "cellular_neighborhood",
                         name = "aggregatedNeighborhood")

# Detect spatial context
sce <- detectSpatialContext(sce, entry = "aggregatedNeighborhood",
                           threshold = 0.9)

plotSpatial(sce, img_id = "ImageNb",
           colPairName = "knn_sc_graph",
           node_color_by = "spatial_context",
           scales = "free")
            
# Plot spatial context - default
plotSpatialContext(sce, group_by = "ImageNb")

# Plot spatial context - adjust aesthetics
plotSpatialContext(sce, group_by = "ImageNb",
                   node_color_by = "name",
                   node_size_by = "n_cells",
                   node_label_color_by = "name")
                   
plotSpatialContext(sce, group_by = "ImageNb",
                   node_color_by = "n_cells",
                   node_size_by = "n_group")
                   
# Plot spatial context - return data
plotSpatialContext(sce, group_by = "ImageNb",
                  return_data = TRUE)          
                  

BodenmillerGroup/imcRtools documentation built on Oct. 30, 2024, 12:19 p.m.