Plot interaction graph

Function to plot directed interaction graphs based on symbolic edge-lists and vertex metadata. The user can specify node, node_label and edge aesthetics using dedicated arguments. The resulting plot can be further refined with `ggplot2` for node styling and `ggraph` for edge-specific customization.

plotInteractions(
  out,
  object,
  label,
  group_by,
  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,
  edge_color_by = NULL,
  edge_color_fix = NULL,
  edge_width_by = NULL,
  edge_width_fix = NULL,
  draw_edges = TRUE,
  return_data = FALSE,
  graph_layout = "circle"
)

Arguments

out: a data frame representing an edge list with columns "group_by", "from_label" and "to_label". Additional columns may be included to specify edge attributes (weight or color).
object: a SingleCellExperiment or SpatialExperiment object.
label: single character specifying the colData(object) entry which stores the cell labels. These can be cell-types labels or other metadata entries.
group_by: a single character indicating the colData(object) entry by which interactions are grouped. This is usually the image or patient ID. a single character indicating the colData(object)
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.
edge_color_by: single character indicating the column name of "out" by which the edges are colored.
edge_color_fix: single character specifying the color of all edges.
edge_width_by: single character indicating the column name of "out" by which the width of the edges are scaled.
edge_width_fix: single numeric specifying the width of all edges.
draw_edges: should edges be drawn between nodes? Defaults to TRUE.
return_data: should the edge list and vertex metadata for graph construction be returned as a list of two data.frames?
graph_layout: single character of "circle", "chord", "linear", "fr", "kk", "drl", "stress", "graphopt", "lgl", "tree", "sugiyama", "star", "nicely", "manual", "grid", "mds", "sphere", "randomly", "gem", "dh" which defines the graph layout. Defaults to "circle". For more information, see ggraph.

Value

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

Author

Marlene Lutz (marlene.lutz@uzh.ch)

Examples

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

## 1. countInteractions or testInteractions
sce  <- buildSpatialGraph(pancreasSCE, img_id = "ImageNb", type = "knn", k = 3)
#> The returned object is ordered by the 'ImageNb' entry.

count_out <- countInteractions(sce,
                               group_by = "ImageNb",
                               label = "CellType",
                               method = "classic", # choose from c("classic", "histocat", "patch", "interaction")
                               colPairName = "knn_interaction_graph")

test_out <- testInteractions(sce, 
                             group_by = "ImageNb",
                             label = "CellType", 
                             method = "classic", # choose from c("classic", "histocat", "patch", "interaction")
                             colPairName = "knn_interaction_graph", 
                             iter = 100, 
                             p_threshold = 0.5, 
                             BPPARAM = SerialParam(RNGseed = 123))

## 2. Plot interactions 

# default                
plotInteractions(count_out, sce, "CellType", "ImageNb")


# adjust node aesthetics
plotInteractions(count_out, sce, "CellType", "ImageNb",
                 node_color_by = "name",
                 node_size_by = "n_cells")

                 
# adjust edge aesthetics
plotInteractions(test_out, sce, "CellType", "ImageNb", 
                 edge_width_by = "ct")

                   
# Plot interactions - return data
plotInteractions(test_out, sce, "CellType", "ImageNb",
                 return_data = TRUE)          
#> $edges
#>    from_label   to_label weight
#> 1  celltype_A celltype_A      1
#> 2  celltype_A celltype_B      1
#> 3  celltype_A celltype_C      1
#> 4  celltype_B celltype_A      1
#> 5  celltype_B celltype_B      1
#> 6  celltype_B celltype_C      1
#> 7  celltype_C celltype_A      1
#> 8  celltype_C celltype_B      1
#> 9  celltype_C celltype_C      1
#> 10 celltype_A celltype_A      1
#> 11 celltype_A celltype_B      1
#> 12 celltype_A celltype_C      1
#> 13 celltype_B celltype_A      1
#> 14 celltype_B celltype_B      1
#> 15 celltype_B celltype_C      1
#> 16 celltype_C celltype_A      1
#> 17 celltype_C celltype_B      1
#> 18 celltype_C celltype_C      1
#> 19 celltype_A celltype_A      1
#> 20 celltype_A celltype_B      1
#> 21 celltype_A celltype_C      1
#> 22 celltype_B celltype_A      1
#> 23 celltype_B celltype_B      1
#> 24 celltype_B celltype_C      1
#> 25 celltype_C celltype_A      1
#> 26 celltype_C celltype_B      1
#> 27 celltype_C celltype_C      1
#> 
#> $vertices
#>     CellType n_cells n_group
#> 1 celltype_A      62       2
#> 2 celltype_B     111       3
#> 3 celltype_C     189       3
#>

Arguments

Value

See also

Author

Examples