spatialCCC

The goal of spatialCCC package is to investigate cell-cell signaling, by analyzing ligand-receptor interactions in spatial transcriptomic data.

Installation

You can install the development version of spatialCCC from GitHub with:

# install.packages("devtools")
devtools::install_github("dolchan/spatialCCC")

Example

This is a basic example which shows you a basic workflow of the package:

• First, load required R packages.

library(spatialCCC)

• Then, load built-in LR database.

set.seed(100)

LRdb_m <- 
  get_LRdb("mouse", n_samples = 100)

• Load an example Visium spatial transcriptomic data

data_dir <- file.path("example", "visium_tutorial")
spe_brain <-
  SpatialExperiment::read10xVisium(samples = data_dir,
                                   type = "HDF5",
                                   data = "filtered")

# Log-Normalize
spe_brain <- scater::logNormCounts(spe_brain)

Cell-cell communication analysis

• Compute Cell-Cell Communications over ligand-receptor pairs

ccc_graph_list <-
  compute_spatial_ccc_graph_list(spe = spe_brain,
                                 assay_name = "logcounts",
                                 LRdb = LRdb_m, 
                                 workers = 6)

Cell-cell commuication visualization

• Spatial CCC graph plot with tissue image

LR_of_interest <- "Pdgfb_Pdgfra"

plot_spatial_ccc_graph(
  ccc_graph = ccc_graph_list[[LR_of_interest]],
  tissue_img = SpatialExperiment::imgRaster(spe_brain),
  node_color = "group",
  node_size = 1,
  node_alpha = 0.5,
  edge_color = "group",
  # clip = TRUE,
  which_on_top = "edge"
)

• Spatial CCC graph plot without tissue image

In this case, graph layout can be “spatial” which keeps the original spatial locations, or other graph layout algorithm supported by igraph package.

plot_spatial_ccc_graph(
  ccc_graph = ccc_graph_list[[LR_of_interest]],
  graph_layout = "spatial",
  node_color =  "group",
  node_size = 1,
  edge_color = "group_diameter",
  clip = TRUE,
  which_on_top = "edge"
)

• Spatial CCC graph plot with “auto”, a.k.a., “kk” spring layout

In this format and the one below, one can see the distribution of cell-cell communication clusters

plot_spatial_ccc_graph(
  ccc_graph = ccc_graph_list[[LR_of_interest]],
  node_color = "group",
  node_size = 0.1,
  edge_color = "group_diameter",
  edge_width = 0.1,
  which_on_top = "edge"
)

• Spatial CCC graph plot with “stress” layout

plot_spatial_ccc_graph(
  ccc_graph = ccc_graph_list[[LR_of_interest]],
  # tissue_img = SpatialExperiment::imgRaster(spe_brain),
  graph_layout = "stress",
  node_color = "group",
  edge_color = "group_diameter",
  edge_width = 0.25,
  which_on_top = "edge"
)